HEADER PROTEIN TRANSPORT 13-SEP-11 3TSO TITLE STRUCTURE OF THE CANCER ASSOCIATED RAB25 PROTEIN IN COMPLEX WITH FIP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-25; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 7-180; COMPND 5 SYNONYM: CATX-8; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAB11 FAMILY-INTERACTING PROTEIN 2; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: UNP RESIDUES 440-512; COMPND 11 SYNONYM: RAB11-FIP2, NRIP11; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB25, CATX8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RAB11FIP2, KIAA0941; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAS GTPASE FOLD (RAB25), VESICLE TRAFFICKING, ENDOSOME, PROTEIN KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.ODA,P.Y.LALL,M.W.MCCAFFREY,A.R.KHAN REVDAT 2 28-FEB-24 3TSO 1 REMARK SEQADV LINK REVDAT 1 19-SEP-12 3TSO 0 JRNL AUTH S.ODA,P.Y.LALL,M.W.MCCAFFREY,A.R.KHAN JRNL TITL STRUCTURE OF THE CANCER ASSOCIATED RAB25 PROTEIN IN COMPLEX JRNL TITL 2 WITH FIP2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 3 NUMBER OF REFLECTIONS : 46358 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 + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2499 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2200 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 58.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3570 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.07000 REMARK 3 B12 (A**2) : -0.04000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : -0.03000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.263 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3742 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5084 ; 1.969 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 450 ; 5.798 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;30.749 ;23.576 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 652 ;15.724 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;19.886 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 603 ; 0.156 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2711 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2234 ; 1.249 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3627 ; 2.112 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1508 ; 3.355 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1457 ; 5.192 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3TSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 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) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50863 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.41100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG8000, 0.1M NA/K PHOSPHATE PH REMARK 280 6.2, 0.2M NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 MET A 6 REMARK 465 GLU A 7 REMARK 465 ASP A 8 REMARK 465 TYR A 9 REMARK 465 LYS A 179 REMARK 465 GLN A 180 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 HIS B 5 REMARK 465 MET B 6 REMARK 465 GLU B 7 REMARK 465 ASP B 8 REMARK 465 TYR B 9 REMARK 465 ASN B 10 REMARK 465 SER B 178 REMARK 465 LYS B 179 REMARK 465 GLN B 180 REMARK 465 SER C 438 REMARK 465 MET C 439 REMARK 465 ASN C 440 REMARK 465 PRO C 441 REMARK 465 PHE C 442 REMARK 465 ASP C 443 REMARK 465 ALA C 444 REMARK 465 THR C 445 REMARK 465 ALA C 446 REMARK 465 GLY C 447 REMARK 465 TYR C 448 REMARK 465 SER C 503 REMARK 465 ARG C 504 REMARK 465 LYS C 505 REMARK 465 ALA C 506 REMARK 465 GLY C 507 REMARK 465 LYS C 508 REMARK 465 PHE C 509 REMARK 465 SER C 510 REMARK 465 ASN C 511 REMARK 465 SER C 512 REMARK 465 SER D 438 REMARK 465 MET D 439 REMARK 465 ASN D 440 REMARK 465 PRO D 441 REMARK 465 PHE D 442 REMARK 465 ASP D 443 REMARK 465 ALA D 444 REMARK 465 THR D 445 REMARK 465 ALA D 446 REMARK 465 GLY D 447 REMARK 465 TYR D 448 REMARK 465 SER D 503 REMARK 465 ARG D 504 REMARK 465 LYS D 505 REMARK 465 ALA D 506 REMARK 465 GLY D 507 REMARK 465 LYS D 508 REMARK 465 PHE D 509 REMARK 465 SER D 510 REMARK 465 ASN D 511 REMARK 465 SER D 512 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 131 CG CD OE1 NE2 REMARK 480 LYS A 176 NZ REMARK 480 ARG B 42 NE CZ NH1 NH2 REMARK 480 GLN C 458 CD OE1 NE2 REMARK 480 ARG D 449 CG CD NE CZ NH1 NH2 REMARK 480 GLN D 458 CD OE1 NE2 REMARK 480 ARG D 468 CD NE CZ NH1 NH2 REMARK 480 ARG D 487 CD NE CZ NH1 NH2 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 O2 PO4 A 205 O HOH A 300 2.13 REMARK 500 OE2 GLU D 465 NH1 ARG D 469 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 42 CD ARG B 42 NE -0.147 REMARK 500 GLN D 458 CG GLN D 458 CD 0.187 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 ARG A 141 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 42 CD - NE - CZ ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG B 105 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 133 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 MET C 489 CG - SD - CE ANGL. DEV. = -14.1 DEGREES REMARK 500 GLN D 458 CB - CG - CD ANGL. DEV. = -16.0 DEGREES REMARK 500 ASP D 479 CB - CG - OD2 ANGL. DEV. = -5.8 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 LYS A 126 40.04 72.75 REMARK 500 SER A 159 -16.54 88.54 REMARK 500 ASN A 161 9.85 59.81 REMARK 500 LYS B 126 33.35 79.44 REMARK 500 LEU B 129 56.01 -96.99 REMARK 500 SER B 159 -9.65 93.65 REMARK 500 THR D 492 70.07 -150.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 26 OG1 REMARK 620 2 THR A 44 OG1 85.0 REMARK 620 3 GNP A 201 O2G 174.1 90.6 REMARK 620 4 GNP A 201 O2B 87.3 171.6 97.3 REMARK 620 5 HOH A 368 O 89.0 93.5 87.4 89.9 REMARK 620 6 HOH A 377 O 90.6 88.0 93.1 88.6 178.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 26 OG1 REMARK 620 2 THR B 44 OG1 82.3 REMARK 620 3 GNP B 201 O2B 89.7 169.6 REMARK 620 4 GNP B 201 O2G 176.7 94.5 93.4 REMARK 620 5 HOH B 352 O 83.4 85.0 87.5 95.6 REMARK 620 6 HOH B 353 O 93.8 92.9 94.1 87.0 176.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 203 DBREF 3TSO A 7 180 UNP P57735 RAB25_HUMAN 7 180 DBREF 3TSO B 7 180 UNP P57735 RAB25_HUMAN 7 180 DBREF 3TSO C 440 512 UNP Q7L804 RFIP2_HUMAN 440 512 DBREF 3TSO D 440 512 UNP Q7L804 RFIP2_HUMAN 440 512 SEQADV 3TSO GLY A 3 UNP P57735 EXPRESSION TAG SEQADV 3TSO SER A 4 UNP P57735 EXPRESSION TAG SEQADV 3TSO HIS A 5 UNP P57735 EXPRESSION TAG SEQADV 3TSO MET A 6 UNP P57735 EXPRESSION TAG SEQADV 3TSO GLY B 3 UNP P57735 EXPRESSION TAG SEQADV 3TSO SER B 4 UNP P57735 EXPRESSION TAG SEQADV 3TSO HIS B 5 UNP P57735 EXPRESSION TAG SEQADV 3TSO MET B 6 UNP P57735 EXPRESSION TAG SEQADV 3TSO SER C 438 UNP Q7L804 EXPRESSION TAG SEQADV 3TSO MET C 439 UNP Q7L804 EXPRESSION TAG SEQADV 3TSO SER D 438 UNP Q7L804 EXPRESSION TAG SEQADV 3TSO MET D 439 UNP Q7L804 EXPRESSION TAG SEQRES 1 A 178 GLY SER HIS MET GLU ASP TYR ASN PHE VAL PHE LYS VAL SEQRES 2 A 178 VAL LEU ILE GLY GLU SER GLY VAL GLY LYS THR ASN LEU SEQRES 3 A 178 LEU SER ARG PHE THR ARG ASN GLU PHE SER HIS ASP SER SEQRES 4 A 178 ARG THR THR ILE GLY VAL GLU PHE SER THR ARG THR VAL SEQRES 5 A 178 MET LEU GLY THR ALA ALA VAL LYS ALA GLN ILE TRP ASP SEQRES 6 A 178 THR ALA GLY LEU GLU ARG TYR ARG ALA ILE THR SER ALA SEQRES 7 A 178 TYR TYR ARG GLY ALA VAL GLY ALA LEU LEU VAL PHE ASP SEQRES 8 A 178 LEU THR LYS HIS GLN THR TYR ALA VAL VAL GLU ARG TRP SEQRES 9 A 178 LEU LYS GLU LEU TYR ASP HIS ALA GLU ALA THR ILE VAL SEQRES 10 A 178 VAL MET LEU VAL GLY ASN LYS SER ASP LEU SER GLN ALA SEQRES 11 A 178 ARG GLU VAL PRO THR GLU GLU ALA ARG MET PHE ALA GLU SEQRES 12 A 178 ASN ASN GLY LEU LEU PHE LEU GLU THR SER ALA LEU ASP SEQRES 13 A 178 SER THR ASN VAL GLU LEU ALA PHE GLU THR VAL LEU LYS SEQRES 14 A 178 GLU ILE PHE ALA LYS VAL SER LYS GLN SEQRES 1 B 178 GLY SER HIS MET GLU ASP TYR ASN PHE VAL PHE LYS VAL SEQRES 2 B 178 VAL LEU ILE GLY GLU SER GLY VAL GLY LYS THR ASN LEU SEQRES 3 B 178 LEU SER ARG PHE THR ARG ASN GLU PHE SER HIS ASP SER SEQRES 4 B 178 ARG THR THR ILE GLY VAL GLU PHE SER THR ARG THR VAL SEQRES 5 B 178 MET LEU GLY THR ALA ALA VAL LYS ALA GLN ILE TRP ASP SEQRES 6 B 178 THR ALA GLY LEU GLU ARG TYR ARG ALA ILE THR SER ALA SEQRES 7 B 178 TYR TYR ARG GLY ALA VAL GLY ALA LEU LEU VAL PHE ASP SEQRES 8 B 178 LEU THR LYS HIS GLN THR TYR ALA VAL VAL GLU ARG TRP SEQRES 9 B 178 LEU LYS GLU LEU TYR ASP HIS ALA GLU ALA THR ILE VAL SEQRES 10 B 178 VAL MET LEU VAL GLY ASN LYS SER ASP LEU SER GLN ALA SEQRES 11 B 178 ARG GLU VAL PRO THR GLU GLU ALA ARG MET PHE ALA GLU SEQRES 12 B 178 ASN ASN GLY LEU LEU PHE LEU GLU THR SER ALA LEU ASP SEQRES 13 B 178 SER THR ASN VAL GLU LEU ALA PHE GLU THR VAL LEU LYS SEQRES 14 B 178 GLU ILE PHE ALA LYS VAL SER LYS GLN SEQRES 1 C 75 SER MET ASN PRO PHE ASP ALA THR ALA GLY TYR ARG SER SEQRES 2 C 75 LEU THR TYR GLU GLU VAL LEU GLN GLU LEU VAL LYS HIS SEQRES 3 C 75 LYS GLU LEU LEU ARG ARG LYS ASP THR HIS ILE ARG GLU SEQRES 4 C 75 LEU GLU ASP TYR ILE ASP ASN LEU LEU VAL ARG VAL MET SEQRES 5 C 75 GLU GLU THR PRO SER ILE LEU ARG VAL PRO TYR GLU PRO SEQRES 6 C 75 SER ARG LYS ALA GLY LYS PHE SER ASN SER SEQRES 1 D 75 SER MET ASN PRO PHE ASP ALA THR ALA GLY TYR ARG SER SEQRES 2 D 75 LEU THR TYR GLU GLU VAL LEU GLN GLU LEU VAL LYS HIS SEQRES 3 D 75 LYS GLU LEU LEU ARG ARG LYS ASP THR HIS ILE ARG GLU SEQRES 4 D 75 LEU GLU ASP TYR ILE ASP ASN LEU LEU VAL ARG VAL MET SEQRES 5 D 75 GLU GLU THR PRO SER ILE LEU ARG VAL PRO TYR GLU PRO SEQRES 6 D 75 SER ARG LYS ALA GLY LYS PHE SER ASN SER HET MG A 200 1 HET GNP A 201 32 HET GOL A 202 6 HET GOL A 203 6 HET GOL A 204 6 HET PO4 A 205 5 HET PO4 A 206 5 HET MG B 200 1 HET GNP B 201 32 HET GOL B 202 6 HET GOL B 203 6 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 MG 2(MG 2+) FORMUL 6 GNP 2(C10 H17 N6 O13 P3) FORMUL 7 GOL 5(C3 H8 O3) FORMUL 10 PO4 2(O4 P 3-) FORMUL 16 HOH *208(H2 O) HELIX 1 1 GLY A 24 ASN A 35 1 12 HELIX 2 2 ILE A 77 ARG A 83 1 7 HELIX 3 3 LYS A 96 VAL A 102 1 7 HELIX 4 4 VAL A 102 ASP A 112 1 11 HELIX 5 5 LYS A 126 ARG A 133 5 8 HELIX 6 6 PRO A 136 ASN A 147 1 12 HELIX 7 7 ASN A 161 SER A 178 1 18 HELIX 8 8 GLY B 24 ASN B 35 1 12 HELIX 9 9 ILE B 77 ARG B 83 1 7 HELIX 10 10 LYS B 96 VAL B 102 1 7 HELIX 11 11 VAL B 102 ALA B 114 1 13 HELIX 12 12 LEU B 129 ARG B 133 5 5 HELIX 13 13 PRO B 136 ASN B 147 1 12 HELIX 14 14 ASN B 161 VAL B 177 1 17 HELIX 15 15 THR C 452 THR C 492 1 41 HELIX 16 16 PRO C 493 ARG C 497 5 5 HELIX 17 17 THR D 452 THR D 492 1 41 HELIX 18 18 PRO D 493 ARG D 497 5 5 SHEET 1 A 6 VAL A 47 LEU A 56 0 SHEET 2 A 6 ALA A 59 THR A 68 -1 O VAL A 61 N VAL A 54 SHEET 3 A 6 PHE A 11 ILE A 18 1 N PHE A 13 O LYS A 62 SHEET 4 A 6 GLY A 87 ASP A 93 1 O LEU A 89 N ILE A 18 SHEET 5 A 6 VAL A 119 ASN A 125 1 O ASN A 125 N PHE A 92 SHEET 6 A 6 LEU A 150 GLU A 153 1 O LEU A 150 N VAL A 120 SHEET 1 B 6 VAL B 47 LEU B 56 0 SHEET 2 B 6 ALA B 59 THR B 68 -1 O VAL B 61 N VAL B 54 SHEET 3 B 6 VAL B 12 ILE B 18 1 N VAL B 15 O TRP B 66 SHEET 4 B 6 GLY B 87 ASP B 93 1 O VAL B 91 N ILE B 18 SHEET 5 B 6 VAL B 119 ASN B 125 1 O ASN B 125 N PHE B 92 SHEET 6 B 6 LEU B 150 GLU B 153 1 O LEU B 150 N LEU B 122 LINK OG1 THR A 26 MG MG A 200 1555 1555 2.06 LINK OG1 THR A 44 MG MG A 200 1555 1555 1.98 LINK MG MG A 200 O2G GNP A 201 1555 1555 1.99 LINK MG MG A 200 O2B GNP A 201 1555 1555 2.01 LINK MG MG A 200 O HOH A 368 1555 1555 2.20 LINK MG MG A 200 O HOH A 377 1555 1555 2.04 LINK OG1 THR B 26 MG MG B 200 1555 1555 2.07 LINK OG1 THR B 44 MG MG B 200 1555 1555 2.13 LINK MG MG B 200 O2B GNP B 201 1555 1555 2.03 LINK MG MG B 200 O2G GNP B 201 1555 1555 2.12 LINK MG MG B 200 O HOH B 352 1555 1555 2.08 LINK MG MG B 200 O HOH B 353 1555 1555 2.07 CISPEP 1 VAL C 498 PRO C 499 0 -6.86 CISPEP 2 VAL D 498 PRO D 499 0 -2.78 SITE 1 AC1 5 THR A 26 THR A 44 GNP A 201 HOH A 368 SITE 2 AC1 5 HOH A 377 SITE 1 AC2 29 SER A 21 GLY A 22 VAL A 23 GLY A 24 SITE 2 AC2 29 LYS A 25 THR A 26 ASN A 27 PHE A 37 SITE 3 AC2 29 SER A 38 HIS A 39 ASP A 40 SER A 41 SITE 4 AC2 29 THR A 43 THR A 44 ALA A 69 GLY A 70 SITE 5 AC2 29 ASN A 125 LYS A 126 ASP A 128 LEU A 129 SITE 6 AC2 29 SER A 155 ALA A 156 LEU A 157 MG A 200 SITE 7 AC2 29 HOH A 329 HOH A 344 HOH A 359 HOH A 368 SITE 8 AC2 29 HOH A 377 SITE 1 AC3 5 ASN A 35 GLU A 36 PHE A 37 ASP B 158 SITE 2 AC3 5 THR B 160 SITE 1 AC4 7 ILE A 45 GLY A 46 LEU A 71 ARG A 73 SITE 2 AC4 7 ARG A 75 ILE D 481 ASP D 482 SITE 1 AC5 9 ILE A 18 ALA A 69 LEU A 71 ARG A 75 SITE 2 AC5 9 THR A 78 TYR A 81 TYR A 82 TRP A 106 SITE 3 AC5 9 GLU A 109 SITE 1 AC6 5 GLU A 163 LEU A 164 GLU A 167 HOH A 300 SITE 2 AC6 5 GLU B 138 SITE 1 AC7 3 TYR A 100 ALA A 101 GLU A 104 SITE 1 AC8 5 THR B 26 THR B 44 GNP B 201 HOH B 352 SITE 2 AC8 5 HOH B 353 SITE 1 AC9 26 SER B 21 GLY B 22 VAL B 23 GLY B 24 SITE 2 AC9 26 LYS B 25 THR B 26 ASN B 27 PHE B 37 SITE 3 AC9 26 SER B 38 HIS B 39 SER B 41 THR B 43 SITE 4 AC9 26 THR B 44 ALA B 69 GLY B 70 ASN B 125 SITE 5 AC9 26 LYS B 126 ASP B 128 LEU B 129 SER B 155 SITE 6 AC9 26 ALA B 156 LEU B 157 MG B 200 HOH B 349 SITE 7 AC9 26 HOH B 352 HOH B 353 SITE 1 BC1 7 ILE B 45 GLY B 46 ARG B 73 ARG B 75 SITE 2 BC1 7 GLU C 478 ILE C 481 ASP C 482 SITE 1 BC2 7 ILE B 18 ALA B 69 LEU B 71 ARG B 75 SITE 2 BC2 7 THR B 78 TRP B 106 GLU B 109 CRYST1 43.310 64.210 65.940 113.25 107.24 99.46 P 1 2 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 0.023089 0.003847 0.010174 0.00000 SCALE2 0.000000 0.015789 0.008424 0.00000 SCALE3 0.000000 0.000000 0.017997 0.00000