HEADER TRANSPORT PROTEIN 28-JUL-08 3DYU TITLE CRYSTAL STRUCTURE OF SNX9PX-BAR (230-595), H32 CAVEAT 3DYU CHIRALITY ERRORS AT RESIDUES A503, A592, A594, C266, C284, CAVEAT 2 3DYU C310, C312, C314. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTING NEXIN-9; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 230-595; COMPND 5 SYNONYM: SH3 AND PX DOMAIN-CONTAINING PROTEIN 1, PROTEIN SDP1, SH3 COMPND 6 AND PX DOMAIN-CONTAINING PROTEIN 3A; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: SNX9, SH3PX1, SH3PXD3A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEXHTB KEYWDS 3-HELIX-BUNDLE, BAR DOMAIN, PX DOMAIN, PHOSPHOPROTEIN, PROTEIN KEYWDS 2 TRANSPORT, SH3 DOMAIN, TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.WANG,H.Y.K.KAAN,H.SONDERMANN REVDAT 5 30-AUG-23 3DYU 1 REMARK REVDAT 4 11-AUG-09 3DYU 1 HEADER REVDAT 3 24-FEB-09 3DYU 1 VERSN REVDAT 2 04-NOV-08 3DYU 1 JRNL REVDAT 1 16-SEP-08 3DYU 0 JRNL AUTH Q.WANG,H.Y.KAAN,R.N.HOODA,S.L.GOH,H.SONDERMANN JRNL TITL STRUCTURE AND PLASTICITY OF ENDOPHILIN AND SORTING NEXIN 9. JRNL REF STRUCTURE V. 16 1574 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18940612 JRNL DOI 10.1016/J.STR.2008.07.016 REMARK 2 REMARK 2 RESOLUTION. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 32734.290 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 13767 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.388 REMARK 3 FREE R VALUE : 0.403 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 682 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 4.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.36 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1739 REMARK 3 BIN R VALUE (WORKING SET) : 0.4610 REMARK 3 BIN FREE R VALUE : 0.5730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 87 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.061 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8931 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 129.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 153.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 17.36000 REMARK 3 B22 (A**2) : 17.36000 REMARK 3 B33 (A**2) : -34.72000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.96 REMARK 3 ESD FROM SIGMAA (A) : 1.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.85 REMARK 3 ESD FROM C-V SIGMAA (A) : 2.54 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.560 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 102.4 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE WAS SOLVED BY MOLECULAR REMARK 3 REPLACEMENT AND NOT REFINED DUE TO VERY LOW RESOLUTION OF THE REMARK 3 DATA COLLECTED. THE ONLY MODIFICATION PERFORMED TO THE OBTAINED REMARK 3 MODEL FROM MOLECULAR REPLACEMENT WAS SOME RIGID BODY ADJUSTMENT REMARK 3 OF HELICAL TIPS AND DOMAINS (RESIDUES 507-548, RESIDUES 230-390, REMARK 3 RESIDUES 391-595) ACCORDING TO THE ELECTRON DENSITY. AUTHORS DID REMARK 3 NOT HAVE ENOUGH DATA TO SEE THE SIDE CHAIN POSITIONS. THE REMARK 3 CLASHES BETWEEN SIDE CHAINS OF SURFACE RESIDUES WERE REMOVED REMARK 3 USING ALTERNATIVE ROTAMER CONFORMATION. REMARK 4 REMARK 4 3DYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048660. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97710 REMARK 200 MONOCHROMATOR : KOHZU HLD8-24 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15467 REMARK 200 RESOLUTION RANGE HIGH (A) : 4.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.10900 REMARK 200 FOR THE DATA SET : 25.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 0.88800 REMARK 200 R SYM FOR SHELL (I) : 0.48300 REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, PHENIX REMARK 200 STARTING MODEL: PDB ENTRIES 2RAK, 3DYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 0.1M TRIS-HCL REMARK 280 PH 8.5, 5% PEG 400, 0.05M MGSO4, 15% XYLITOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 65.88250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.03728 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 189.69067 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 65.88250 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 38.03728 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 189.69067 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 65.88250 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 38.03728 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 189.69067 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 65.88250 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 38.03728 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 189.69067 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 65.88250 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 38.03728 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 189.69067 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 65.88250 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 38.03728 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 189.69067 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 76.07456 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 379.38133 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 76.07456 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 379.38133 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 76.07456 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 379.38133 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 76.07456 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 379.38133 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 76.07456 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 379.38133 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 76.07456 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 379.38133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 -65.88250 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 38.03728 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 189.69067 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ARG C 258 N GLU C 271 2.01 REMARK 500 OE1 GLU A 396 NZ LYS A 518 2.15 REMARK 500 NH1 ARG A 568 CD1 LEU B 589 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU C 579 OE2 GLU C 579 10455 1.88 REMARK 500 OE2 GLU C 457 NH2 ARG C 559 10455 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 263 N - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 GLN A 314 N - CA - C ANGL. DEV. = 20.5 DEGREES REMARK 500 PHE A 319 N - CA - C ANGL. DEV. = 19.1 DEGREES REMARK 500 LEU A 390 CA - C - N ANGL. DEV. = 19.0 DEGREES REMARK 500 LEU A 390 O - C - N ANGL. DEV. = -19.9 DEGREES REMARK 500 ASP A 391 C - N - CA ANGL. DEV. = 22.2 DEGREES REMARK 500 GLN B 314 N - CA - C ANGL. DEV. = 20.6 DEGREES REMARK 500 PHE B 319 N - CA - C ANGL. DEV. = 19.2 DEGREES REMARK 500 PRO C 257 C - N - CD ANGL. DEV. = -18.2 DEGREES REMARK 500 PRO C 311 C - N - CD ANGL. DEV. = -16.9 DEGREES REMARK 500 PHE C 319 N - CA - C ANGL. DEV. = 19.1 DEGREES REMARK 500 LEU C 548 CA - C - N ANGL. DEV. = -17.4 DEGREES REMARK 500 LEU C 548 O - C - N ANGL. DEV. = 17.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 251 -166.07 -115.59 REMARK 500 ALA A 255 -163.89 -162.05 REMARK 500 PRO A 257 97.57 -52.56 REMARK 500 MET A 263 26.22 16.46 REMARK 500 LEU A 266 62.22 -105.56 REMARK 500 LYS A 267 47.87 -146.72 REMARK 500 ASN A 280 -1.68 63.76 REMARK 500 ALA A 304 -32.43 -142.30 REMARK 500 ASP A 312 173.92 -51.51 REMARK 500 GLN A 314 -175.14 -49.23 REMARK 500 VAL A 315 32.23 -52.79 REMARK 500 GLU A 321 -73.64 -37.08 REMARK 500 LEU A 354 -79.21 -84.31 REMARK 500 PRO A 388 -169.59 -70.94 REMARK 500 THR A 458 -40.43 176.20 REMARK 500 ASP A 485 -58.72 -149.76 REMARK 500 PHE A 503 -79.34 4.18 REMARK 500 PRO A 504 -74.41 -107.79 REMARK 500 ASP A 505 -64.95 0.32 REMARK 500 LEU A 548 -74.11 -71.71 REMARK 500 GLN A 549 -48.31 -22.41 REMARK 500 SER A 590 30.90 -62.99 REMARK 500 PHE A 592 114.59 1.45 REMARK 500 VAL A 594 -12.81 36.40 REMARK 500 ASP B 251 -166.12 -115.68 REMARK 500 ALA B 255 -163.84 -162.05 REMARK 500 PRO B 257 97.52 -52.65 REMARK 500 LYS B 262 69.49 -166.04 REMARK 500 MET B 263 94.22 21.63 REMARK 500 TYR B 264 0.69 -151.12 REMARK 500 LEU B 266 62.19 -109.02 REMARK 500 LYS B 267 47.81 -146.73 REMARK 500 ASN B 280 -1.65 63.86 REMARK 500 ALA B 304 -32.22 -142.41 REMARK 500 ASP B 312 173.76 -51.48 REMARK 500 GLN B 314 -175.21 -49.13 REMARK 500 VAL B 315 32.41 -52.95 REMARK 500 GLU B 321 -73.53 -37.24 REMARK 500 LEU B 354 -79.15 -84.40 REMARK 500 PRO B 388 -169.64 -70.79 REMARK 500 ASP B 391 163.98 -40.77 REMARK 500 THR B 458 -40.50 176.26 REMARK 500 ASP B 485 -58.73 -149.78 REMARK 500 SER B 590 30.71 -62.83 REMARK 500 VAL B 594 39.00 -40.00 REMARK 500 ASP C 251 -166.07 -115.58 REMARK 500 ASP C 256 130.09 42.89 REMARK 500 MET C 263 81.84 7.21 REMARK 500 TYR C 264 -27.01 -165.07 REMARK 500 LEU C 266 -63.73 24.78 REMARK 500 REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 503 PRO A 504 -109.14 REMARK 500 PRO A 504 ASP A 505 128.36 REMARK 500 GLY A 508 THR A 509 145.06 REMARK 500 ARG A 591 PHE A 592 122.73 REMARK 500 PHE A 592 PRO A 593 131.25 REMARK 500 PRO A 593 VAL A 594 78.57 REMARK 500 GLY B 260 SER B 261 -139.70 REMARK 500 PRO B 593 VAL B 594 137.38 REMARK 500 VAL B 594 MET B 595 130.35 REMARK 500 ALA C 255 ASP C 256 88.52 REMARK 500 ARG C 258 LYS C 259 138.23 REMARK 500 LYS C 259 GLY C 260 75.09 REMARK 500 GLY C 260 SER C 261 137.93 REMARK 500 TYR C 264 GLY C 265 125.14 REMARK 500 GLY C 265 LEU C 266 101.77 REMARK 500 LEU C 266 LYS C 267 -128.63 REMARK 500 VAL C 283 ASN C 284 139.80 REMARK 500 ASN C 284 HIS C 285 -87.95 REMARK 500 LEU C 310 PRO C 311 -143.12 REMARK 500 PRO C 311 ASP C 312 88.87 REMARK 500 ASP C 312 LYS C 313 59.94 REMARK 500 GLN C 314 VAL C 315 131.00 REMARK 500 ASP C 389 LEU C 390 119.47 REMARK 500 ASP C 391 LEU C 392 -131.27 REMARK 500 VAL C 594 MET C 595 143.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DYT RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT HIGH RESOLUTION AND IN SPACE GROUP C2221 DBREF 3DYU A 230 595 UNP Q9Y5X1 SNX9_HUMAN 230 595 DBREF 3DYU B 230 595 UNP Q9Y5X1 SNX9_HUMAN 230 595 DBREF 3DYU C 230 595 UNP Q9Y5X1 SNX9_HUMAN 230 595 SEQRES 1 A 366 GLU LYS ILE PRO ILE ILE VAL GLY ASP TYR GLY PRO MET SEQRES 2 A 366 TRP VAL TYR PRO THR SER THR PHE ASP CYS VAL VAL ALA SEQRES 3 A 366 ASP PRO ARG LYS GLY SER LYS MET TYR GLY LEU LYS SER SEQRES 4 A 366 TYR ILE GLU TYR GLN LEU THR PRO THR ASN THR ASN ARG SEQRES 5 A 366 SER VAL ASN HIS ARG TYR LYS HIS PHE ASP TRP LEU TYR SEQRES 6 A 366 GLU ARG LEU LEU VAL LYS PHE GLY SER ALA ILE PRO ILE SEQRES 7 A 366 PRO SER LEU PRO ASP LYS GLN VAL THR GLY ARG PHE GLU SEQRES 8 A 366 GLU GLU PHE ILE LYS MET ARG MET GLU ARG LEU GLN ALA SEQRES 9 A 366 TRP MET THR ARG MET CYS ARG HIS PRO VAL ILE SER GLU SEQRES 10 A 366 SER GLU VAL PHE GLN GLN PHE LEU ASN PHE ARG ASP GLU SEQRES 11 A 366 LYS GLU TRP LYS THR GLY LYS ARG LYS ALA GLU ARG ASP SEQRES 12 A 366 GLU LEU ALA GLY VAL MET ILE PHE SER THR MET GLU PRO SEQRES 13 A 366 GLU ALA PRO ASP LEU ASP LEU VAL GLU ILE GLU GLN LYS SEQRES 14 A 366 CYS GLU ALA VAL GLY LYS PHE THR LYS ALA MET ASP ASP SEQRES 15 A 366 GLY VAL LYS GLU LEU LEU THR VAL GLY GLN GLU HIS TRP SEQRES 16 A 366 LYS ARG CYS THR GLY PRO LEU PRO LYS GLU TYR GLN LYS SEQRES 17 A 366 ILE GLY LYS ALA LEU GLN SER LEU ALA THR VAL PHE SER SEQRES 18 A 366 SER SER GLY TYR GLN GLY GLU THR ASP LEU ASN ASP ALA SEQRES 19 A 366 ILE THR GLU ALA GLY LYS THR TYR GLU GLU ILE ALA SER SEQRES 20 A 366 LEU VAL ALA GLU GLN PRO LYS LYS ASP LEU HIS PHE LEU SEQRES 21 A 366 MET GLU CYS ASN HIS GLU TYR LYS GLY PHE LEU GLY CYS SEQRES 22 A 366 PHE PRO ASP ILE ILE GLY THR HIS LYS GLY ALA ILE GLU SEQRES 23 A 366 LYS VAL LYS GLU SER ASP LYS LEU VAL ALA THR SER LYS SEQRES 24 A 366 ILE THR LEU GLN ASP LYS GLN ASN MET VAL LYS ARG VAL SEQRES 25 A 366 SER ILE MET SER TYR ALA LEU GLN ALA GLU MET ASN HIS SEQRES 26 A 366 PHE HIS SER ASN ARG ILE TYR ASP TYR ASN SER VAL ILE SEQRES 27 A 366 ARG LEU TYR LEU GLU GLN GLN VAL GLN PHE TYR GLU THR SEQRES 28 A 366 ILE ALA GLU LYS LEU ARG GLN ALA LEU SER ARG PHE PRO SEQRES 29 A 366 VAL MET SEQRES 1 B 366 GLU LYS ILE PRO ILE ILE VAL GLY ASP TYR GLY PRO MET SEQRES 2 B 366 TRP VAL TYR PRO THR SER THR PHE ASP CYS VAL VAL ALA SEQRES 3 B 366 ASP PRO ARG LYS GLY SER LYS MET TYR GLY LEU LYS SER SEQRES 4 B 366 TYR ILE GLU TYR GLN LEU THR PRO THR ASN THR ASN ARG SEQRES 5 B 366 SER VAL ASN HIS ARG TYR LYS HIS PHE ASP TRP LEU TYR SEQRES 6 B 366 GLU ARG LEU LEU VAL LYS PHE GLY SER ALA ILE PRO ILE SEQRES 7 B 366 PRO SER LEU PRO ASP LYS GLN VAL THR GLY ARG PHE GLU SEQRES 8 B 366 GLU GLU PHE ILE LYS MET ARG MET GLU ARG LEU GLN ALA SEQRES 9 B 366 TRP MET THR ARG MET CYS ARG HIS PRO VAL ILE SER GLU SEQRES 10 B 366 SER GLU VAL PHE GLN GLN PHE LEU ASN PHE ARG ASP GLU SEQRES 11 B 366 LYS GLU TRP LYS THR GLY LYS ARG LYS ALA GLU ARG ASP SEQRES 12 B 366 GLU LEU ALA GLY VAL MET ILE PHE SER THR MET GLU PRO SEQRES 13 B 366 GLU ALA PRO ASP LEU ASP LEU VAL GLU ILE GLU GLN LYS SEQRES 14 B 366 CYS GLU ALA VAL GLY LYS PHE THR LYS ALA MET ASP ASP SEQRES 15 B 366 GLY VAL LYS GLU LEU LEU THR VAL GLY GLN GLU HIS TRP SEQRES 16 B 366 LYS ARG CYS THR GLY PRO LEU PRO LYS GLU TYR GLN LYS SEQRES 17 B 366 ILE GLY LYS ALA LEU GLN SER LEU ALA THR VAL PHE SER SEQRES 18 B 366 SER SER GLY TYR GLN GLY GLU THR ASP LEU ASN ASP ALA SEQRES 19 B 366 ILE THR GLU ALA GLY LYS THR TYR GLU GLU ILE ALA SER SEQRES 20 B 366 LEU VAL ALA GLU GLN PRO LYS LYS ASP LEU HIS PHE LEU SEQRES 21 B 366 MET GLU CYS ASN HIS GLU TYR LYS GLY PHE LEU GLY CYS SEQRES 22 B 366 PHE PRO ASP ILE ILE GLY THR HIS LYS GLY ALA ILE GLU SEQRES 23 B 366 LYS VAL LYS GLU SER ASP LYS LEU VAL ALA THR SER LYS SEQRES 24 B 366 ILE THR LEU GLN ASP LYS GLN ASN MET VAL LYS ARG VAL SEQRES 25 B 366 SER ILE MET SER TYR ALA LEU GLN ALA GLU MET ASN HIS SEQRES 26 B 366 PHE HIS SER ASN ARG ILE TYR ASP TYR ASN SER VAL ILE SEQRES 27 B 366 ARG LEU TYR LEU GLU GLN GLN VAL GLN PHE TYR GLU THR SEQRES 28 B 366 ILE ALA GLU LYS LEU ARG GLN ALA LEU SER ARG PHE PRO SEQRES 29 B 366 VAL MET SEQRES 1 C 366 GLU LYS ILE PRO ILE ILE VAL GLY ASP TYR GLY PRO MET SEQRES 2 C 366 TRP VAL TYR PRO THR SER THR PHE ASP CYS VAL VAL ALA SEQRES 3 C 366 ASP PRO ARG LYS GLY SER LYS MET TYR GLY LEU LYS SER SEQRES 4 C 366 TYR ILE GLU TYR GLN LEU THR PRO THR ASN THR ASN ARG SEQRES 5 C 366 SER VAL ASN HIS ARG TYR LYS HIS PHE ASP TRP LEU TYR SEQRES 6 C 366 GLU ARG LEU LEU VAL LYS PHE GLY SER ALA ILE PRO ILE SEQRES 7 C 366 PRO SER LEU PRO ASP LYS GLN VAL THR GLY ARG PHE GLU SEQRES 8 C 366 GLU GLU PHE ILE LYS MET ARG MET GLU ARG LEU GLN ALA SEQRES 9 C 366 TRP MET THR ARG MET CYS ARG HIS PRO VAL ILE SER GLU SEQRES 10 C 366 SER GLU VAL PHE GLN GLN PHE LEU ASN PHE ARG ASP GLU SEQRES 11 C 366 LYS GLU TRP LYS THR GLY LYS ARG LYS ALA GLU ARG ASP SEQRES 12 C 366 GLU LEU ALA GLY VAL MET ILE PHE SER THR MET GLU PRO SEQRES 13 C 366 GLU ALA PRO ASP LEU ASP LEU VAL GLU ILE GLU GLN LYS SEQRES 14 C 366 CYS GLU ALA VAL GLY LYS PHE THR LYS ALA MET ASP ASP SEQRES 15 C 366 GLY VAL LYS GLU LEU LEU THR VAL GLY GLN GLU HIS TRP SEQRES 16 C 366 LYS ARG CYS THR GLY PRO LEU PRO LYS GLU TYR GLN LYS SEQRES 17 C 366 ILE GLY LYS ALA LEU GLN SER LEU ALA THR VAL PHE SER SEQRES 18 C 366 SER SER GLY TYR GLN GLY GLU THR ASP LEU ASN ASP ALA SEQRES 19 C 366 ILE THR GLU ALA GLY LYS THR TYR GLU GLU ILE ALA SER SEQRES 20 C 366 LEU VAL ALA GLU GLN PRO LYS LYS ASP LEU HIS PHE LEU SEQRES 21 C 366 MET GLU CYS ASN HIS GLU TYR LYS GLY PHE LEU GLY CYS SEQRES 22 C 366 PHE PRO ASP ILE ILE GLY THR HIS LYS GLY ALA ILE GLU SEQRES 23 C 366 LYS VAL LYS GLU SER ASP LYS LEU VAL ALA THR SER LYS SEQRES 24 C 366 ILE THR LEU GLN ASP LYS GLN ASN MET VAL LYS ARG VAL SEQRES 25 C 366 SER ILE MET SER TYR ALA LEU GLN ALA GLU MET ASN HIS SEQRES 26 C 366 PHE HIS SER ASN ARG ILE TYR ASP TYR ASN SER VAL ILE SEQRES 27 C 366 ARG LEU TYR LEU GLU GLN GLN VAL GLN PHE TYR GLU THR SEQRES 28 C 366 ILE ALA GLU LYS LEU ARG GLN ALA LEU SER ARG PHE PRO SEQRES 29 C 366 VAL MET HELIX 1 1 TYR A 287 GLY A 302 1 16 HELIX 2 2 GLU A 320 ARG A 340 1 21 HELIX 3 3 SER A 347 ASN A 355 1 9 HELIX 4 4 LYS A 360 ARG A 371 1 12 HELIX 5 5 ALA A 375 SER A 381 5 7 HELIX 6 6 ASP A 391 THR A 428 1 38 HELIX 7 7 GLY A 429 SER A 450 1 22 HELIX 8 8 THR A 458 GLU A 480 1 23 HELIX 9 9 GLN A 481 LYS A 484 5 4 HELIX 10 10 ASP A 485 CYS A 502 1 18 HELIX 11 11 PHE A 503 GLY A 508 5 6 HELIX 12 12 THR A 509 VAL A 517 1 9 HELIX 13 13 LYS A 518 THR A 526 1 9 HELIX 14 14 THR A 530 SER A 590 1 61 HELIX 15 15 TYR B 287 GLY B 302 1 16 HELIX 16 16 GLU B 320 ARG B 340 1 21 HELIX 17 17 SER B 347 ASN B 355 1 9 HELIX 18 18 LYS B 360 ARG B 371 1 12 HELIX 19 19 ALA B 375 SER B 381 5 7 HELIX 20 20 ASP B 391 THR B 428 1 38 HELIX 21 21 GLY B 429 SER B 450 1 22 HELIX 22 22 THR B 458 GLU B 480 1 23 HELIX 23 23 GLN B 481 LYS B 484 5 4 HELIX 24 24 ASP B 485 CYS B 502 1 18 HELIX 25 25 CYS B 502 VAL B 517 1 16 HELIX 26 26 LYS B 518 THR B 526 1 9 HELIX 27 27 THR B 530 SER B 590 1 61 HELIX 28 28 ARG C 286 GLY C 302 1 17 HELIX 29 29 GLU C 320 ARG C 340 1 21 HELIX 30 30 SER C 347 ASN C 355 1 9 HELIX 31 31 LYS C 360 ARG C 371 1 12 HELIX 32 32 ALA C 375 SER C 381 5 7 HELIX 33 33 ASP C 391 THR C 428 1 38 HELIX 34 34 GLY C 429 SER C 450 1 22 HELIX 35 35 THR C 458 GLU C 480 1 23 HELIX 36 36 GLN C 481 LYS C 484 5 4 HELIX 37 37 ASP C 485 CYS C 502 1 18 HELIX 38 38 CYS C 502 VAL C 517 1 16 HELIX 39 39 LYS C 518 THR C 526 1 9 HELIX 40 40 THR C 530 SER C 590 1 61 SHEET 1 A 3 MET A 242 TRP A 243 0 SHEET 2 A 3 ILE A 232 ILE A 235 -1 N ILE A 235 O MET A 242 SHEET 3 A 3 MET A 383 PRO A 385 1 O GLU A 384 N ILE A 232 SHEET 1 B 3 CYS A 252 LYS A 259 0 SHEET 2 B 3 ILE A 270 PRO A 276 -1 O GLU A 271 N ARG A 258 SHEET 3 B 3 VAL A 283 ARG A 286 -1 O HIS A 285 N TYR A 272 SHEET 1 C 3 MET B 242 TRP B 243 0 SHEET 2 C 3 ILE B 232 ILE B 235 -1 N ILE B 235 O MET B 242 SHEET 3 C 3 MET B 383 PRO B 385 1 O GLU B 384 N ILE B 232 SHEET 1 D 3 CYS B 252 LYS B 259 0 SHEET 2 D 3 ILE B 270 PRO B 276 -1 O GLU B 271 N ARG B 258 SHEET 3 D 3 VAL B 283 ARG B 286 -1 O HIS B 285 N TYR B 272 SHEET 1 E 3 MET C 242 TRP C 243 0 SHEET 2 E 3 ILE C 232 ILE C 235 -1 N ILE C 235 O MET C 242 SHEET 3 E 3 MET C 383 PRO C 385 1 O GLU C 384 N ILE C 232 SHEET 1 F 2 CYS C 252 VAL C 254 0 SHEET 2 F 2 LEU C 274 PRO C 276 -1 O THR C 275 N VAL C 253 CISPEP 1 SER C 309 LEU C 310 0 8.12 CRYST1 131.765 131.765 569.072 90.00 90.00 120.00 H 3 2 54 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007589 0.004382 0.000000 0.00000 SCALE2 0.000000 0.008763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001757 0.00000