HEADER TRANSPORT PROTEIN 29-AUG-14 4UYB TITLE CRYSTAL STRUCTURE OF SEC14-LIKE PROTEIN 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEC14-LIKE PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SEC14L3C, TOCOPHEROL-ASSOCIATED PROTEIN 2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA KEYWDS TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.KOPEC,S.GOUBIN,T.KROJER,N.BURGESS-BROWN,F.VON DELFT,C.ARROWSMITH, AUTHOR 2 A.EDWARDS,C.BOUNTRA,W.W.YUE REVDAT 3 10-JAN-24 4UYB 1 REMARK REVDAT 2 24-JAN-18 4UYB 1 JRNL REMARK REVDAT 1 24-SEP-14 4UYB 0 JRNL AUTH J.KOPEC,S.GOUBIN,T.KROJER,N.BURGESS-BROWN,F.VON DELFT, JRNL AUTH 2 C.ARROWSMITH,A.EDWARDS,C.BOUNTRA,W.W.YUE JRNL TITL CRYSTAL STRUCTURE OF SEC14-LIKE PROTEIN 3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 93572 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4973 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6784 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 397 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3242 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 492 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.25000 REMARK 3 B22 (A**2) : -1.25000 REMARK 3 B33 (A**2) : 2.49000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.057 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.056 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.044 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.701 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3646 ; 0.032 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3500 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4941 ; 2.571 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8089 ; 1.717 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 454 ; 5.731 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;34.413 ;24.220 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 652 ;11.628 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.604 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 523 ; 0.159 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4131 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 833 ; 0.002 ; 0.020 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): 1748 ; 2.472 ; 1.777 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1747 ; 2.427 ; 1.774 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2199 ; 3.102 ; 2.685 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2200 ; 3.107 ; 2.687 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1898 ; 3.970 ; 2.202 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1899 ; 3.969 ; 2.203 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2734 ; 4.637 ; 3.150 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 15604 ; 5.268 ;18.510 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 15605 ; 5.268 ;18.511 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7146 ; 4.759 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 59 ;44.991 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7485 ;19.407 ; 5.000 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 : 1.20 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. U VALUES REFINED INDIVIDUALLY. THERE IS AN UNKNOWN REMARK 3 COMPOUND BOUND IN THE STRUCTURE. BISPHENOL IS MODELLED AS IT REMARK 3 FITS NICELY INTO THE DENSITY. IT MUST HAVE BEEN PICKED UP FROM REMARK 3 EXPRESSION, PURIFICATION, CRYSTALLIZATION. REMARK 4 REMARK 4 4UYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1290061640. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 98631 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 83.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 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: PDB ENTRY 1OLM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG6000, 0.8M LITHIUM CHLORIDE, REMARK 280 0.1M CITRATE PH 4.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 87.18150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.62150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.62150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.59075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.62150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.62150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 130.77225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.62150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.62150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.59075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.62150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.62150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 130.77225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 87.18150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 226 CG CD OE1 OE2 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 24 CB CG CD OE1 NE2 REMARK 480 ASP A 25 CB CG OD1 OD2 REMARK 480 VAL A 26 CB CG1 CG2 REMARK 480 LEU A 27 CB CG CD1 CD2 REMARK 480 PRO A 28 CB CG CD 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 OD2 ASP A 34 O HOH A 2064 1.39 REMARK 500 OD1 ASN A 46 O HOH A 2097 1.52 REMARK 500 NZ LYS A 216 O HOH A 2287 1.87 REMARK 500 NZ LYS A 266 O HOH A 2369 2.00 REMARK 500 CD1 LEU A 132 O HOH A 2233 2.01 REMARK 500 O HOH A 2419 O HOH A 2486 2.08 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 O GLY A 287 O HOH A 2058 7455 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 GLU A 14 CD GLU A 14 OE2 0.097 REMARK 500 PRO A 28 CD PRO A 28 N 0.118 REMARK 500 ALA A 29 CA ALA A 29 CB 0.131 REMARK 500 ARG A 40 NE ARG A 40 CZ 0.105 REMARK 500 ARG A 40 CZ ARG A 40 NH2 0.090 REMARK 500 LYS A 51 CE LYS A 51 NZ -0.181 REMARK 500 GLU A 61 CD GLU A 61 OE1 0.081 REMARK 500 THR A 65 CB THR A 65 OG1 -0.139 REMARK 500 GLU A 78 CD GLU A 78 OE2 0.069 REMARK 500 TYR A 91 CE1 TYR A 91 CZ -0.079 REMARK 500 GLN A 118 CG GLN A 118 CD 0.167 REMARK 500 GLU A 147 CD GLU A 147 OE1 -0.068 REMARK 500 GLU A 179 CD GLU A 179 OE2 -0.072 REMARK 500 TYR A 182 CZ TYR A 182 CE2 -0.099 REMARK 500 GLU A 184 CD GLU A 184 OE1 0.070 REMARK 500 VAL A 192 CB VAL A 192 CG2 -0.128 REMARK 500 ARG A 214 CD ARG A 214 NE -0.104 REMARK 500 GLU A 235 CD GLU A 235 OE2 0.089 REMARK 500 GLN A 240 CD GLN A 240 OE1 0.169 REMARK 500 GLN A 240 CD GLN A 240 NE2 -0.189 REMARK 500 VAL A 274 CB VAL A 274 CG2 -0.160 REMARK 500 ARG A 286 CG ARG A 286 CD 0.162 REMARK 500 ARG A 286 CD ARG A 286 NE -0.110 REMARK 500 ARG A 286 CD ARG A 286 NE -0.239 REMARK 500 ARG A 286 NE ARG A 286 CZ 0.120 REMARK 500 GLY A 287 CA GLY A 287 C 0.102 REMARK 500 GLU A 293 CD GLU A 293 OE1 0.075 REMARK 500 TYR A 294 CG TYR A 294 CD1 0.083 REMARK 500 GLU A 295 CD GLU A 295 OE2 0.087 REMARK 500 GLU A 332 CD GLU A 332 OE2 -0.097 REMARK 500 ARG A 364 CD ARG A 364 NE 0.103 REMARK 500 TYR A 393 CG TYR A 393 CD1 0.122 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 ASP A 25 N - CA - CB ANGL. DEV. = -20.1 DEGREES REMARK 500 ASP A 25 CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 PRO A 28 C - N - CD ANGL. DEV. = -13.9 DEGREES REMARK 500 ALA A 29 CB - CA - C ANGL. DEV. = 9.1 DEGREES REMARK 500 ASP A 35 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 TYR A 83 CG - CD1 - CE1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ASP A 101 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 LEU A 106 CA - CB - CG ANGL. DEV. = 16.4 DEGREES REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 126 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 LEU A 132 CB - CG - CD1 ANGL. DEV. = -11.2 DEGREES REMARK 500 LEU A 132 CB - CG - CD2 ANGL. DEV. = 22.1 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 TYR A 171 CB - CG - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 TYR A 182 CD1 - CE1 - CZ ANGL. DEV. = -5.8 DEGREES REMARK 500 GLU A 235 OE1 - CD - OE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 271 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 286 NH1 - CZ - NH2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 286 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 286 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 286 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 TYR A 294 CD1 - CE1 - CZ ANGL. DEV. = 5.6 DEGREES REMARK 500 MET A 346 CG - SD - CE ANGL. DEV. = 12.0 DEGREES REMARK 500 SER A 370 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 PHE A 371 N - CA - C ANGL. DEV. = -18.4 DEGREES REMARK 500 VAL A 372 CG1 - CB - CG2 ANGL. DEV. = 12.9 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 ASN A 32 73.95 -160.61 REMARK 500 PRO A 33 49.44 -79.33 REMARK 500 GLU A 147 13.00 -143.62 REMARK 500 ASN A 223 35.83 -97.17 REMARK 500 PHE A 371 37.16 -151.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE A 284 -11.39 REMARK 500 SER A 370 16.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2070 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A2130 DISTANCE = 5.81 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 UNKNOWN (UNL): TAKEN UP DURING EXPRESSION,PURIFICATION, REMARK 600 CRYSTALLIZATION REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1406 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS MUTATION D TO E POSITION 336 DUE TO ENTRY CLONE REMARK 999 (IMAGE 40006377) DBREF 4UYB A 1 400 UNP Q9UDX4 S14L3_HUMAN 1 400 SEQADV 4UYB SER A 0 UNP Q9UDX4 EXPRESSION TAG SEQADV 4UYB GLU A 335 UNP Q9UDX4 ASP 335 CLONING ARTIFACT SEQRES 1 A 401 SER MET SER GLY ARG VAL GLY ASP LEU SER PRO LYS GLN SEQRES 2 A 401 ALA GLU THR LEU ALA LYS PHE ARG GLU ASN VAL GLN ASP SEQRES 3 A 401 VAL LEU PRO ALA LEU PRO ASN PRO ASP ASP TYR PHE LEU SEQRES 4 A 401 LEU ARG TRP LEU ARG ALA ARG ASN PHE ASP LEU GLN LYS SEQRES 5 A 401 SER GLU ALA LEU LEU ARG LYS TYR MET GLU PHE ARG LYS SEQRES 6 A 401 THR MET ASP ILE ASP HIS ILE LEU ASP TRP GLN PRO PRO SEQRES 7 A 401 GLU VAL ILE GLN LYS TYR MET PRO GLY GLY LEU CYS GLY SEQRES 8 A 401 TYR ASP ARG ASP GLY CYS PRO VAL TRP TYR ASP ILE ILE SEQRES 9 A 401 GLY PRO LEU ASP PRO LYS GLY LEU LEU PHE SER VAL THR SEQRES 10 A 401 LYS GLN ASP LEU LEU LYS THR LYS MET ARG ASP CYS GLU SEQRES 11 A 401 ARG ILE LEU HIS GLU CYS ASP LEU GLN THR GLU ARG LEU SEQRES 12 A 401 GLY LYS LYS ILE GLU THR ILE VAL MET ILE PHE ASP CYS SEQRES 13 A 401 GLU GLY LEU GLY LEU LYS HIS PHE TRP LYS PRO LEU VAL SEQRES 14 A 401 GLU VAL TYR GLN GLU PHE PHE GLY LEU LEU GLU GLU ASN SEQRES 15 A 401 TYR PRO GLU THR LEU LYS PHE MET LEU ILE VAL LYS ALA SEQRES 16 A 401 THR LYS LEU PHE PRO VAL GLY TYR ASN LEU MET LYS PRO SEQRES 17 A 401 PHE LEU SER GLU ASP THR ARG ARG LYS ILE ILE VAL LEU SEQRES 18 A 401 GLY ASN ASN TRP LYS GLU GLY LEU LEU LYS LEU ILE SER SEQRES 19 A 401 PRO GLU GLU LEU PRO ALA GLN PHE GLY GLY THR LEU THR SEQRES 20 A 401 ASP PRO ASP GLY ASN PRO LYS CYS LEU THR LYS ILE ASN SEQRES 21 A 401 TYR GLY GLY GLU ILE PRO LYS SER MET TYR VAL ARG ASP SEQRES 22 A 401 GLN VAL LYS THR GLN TYR GLU HIS SER VAL GLN ILE ASN SEQRES 23 A 401 ARG GLY SER SER HIS GLN VAL GLU TYR GLU ILE LEU PHE SEQRES 24 A 401 PRO GLY CYS VAL LEU ARG TRP GLN PHE SER SER ASP GLY SEQRES 25 A 401 ALA ASP ILE GLY PHE GLY VAL PHE LEU LYS THR LYS MET SEQRES 26 A 401 GLY GLU ARG GLN ARG ALA GLY GLU MET THR GLU VAL LEU SEQRES 27 A 401 PRO SER GLN ARG TYR ASN ALA HIS MET VAL PRO GLU ASP SEQRES 28 A 401 GLY ASN LEU THR CYS SER GLU ALA GLY VAL TYR VAL LEU SEQRES 29 A 401 ARG PHE ASP ASN THR TYR SER PHE VAL HIS ALA LYS LYS SEQRES 30 A 401 VAL SER PHE THR VAL GLU VAL LEU LEU PRO ASP GLU GLY SEQRES 31 A 401 MET GLN LYS TYR ASP LYS GLU LEU THR PRO VAL HET EDO A1401 4 HET EDO A1402 4 HET EDO A1403 4 HET EDO A1404 4 HET EDO A1405 4 HET EDO A1406 4 HET UNL A1407 16 HETNAM EDO 1,2-ETHANEDIOL HETNAM UNL UNKNOWN LIGAND HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 6(C2 H6 O2) FORMUL 9 HOH *492(H2 O) HELIX 1 1 SER A 9 GLN A 24 1 16 HELIX 2 2 VAL A 26 LEU A 30 5 5 HELIX 3 3 ASP A 34 ARG A 45 1 12 HELIX 4 4 ASP A 48 MET A 66 1 19 HELIX 5 5 ASP A 67 TRP A 74 5 8 HELIX 6 6 PRO A 77 MET A 84 1 8 HELIX 7 7 ASP A 107 PHE A 113 1 7 HELIX 8 8 THR A 116 GLY A 143 1 28 HELIX 9 9 GLY A 159 PHE A 163 5 5 HELIX 10 10 TRP A 164 TYR A 182 1 19 HELIX 11 11 LEU A 197 LYS A 206 1 10 HELIX 12 12 PRO A 207 LEU A 209 5 3 HELIX 13 13 SER A 210 LYS A 216 1 7 HELIX 14 14 ASN A 223 ILE A 232 1 10 HELIX 15 15 SER A 233 LEU A 237 5 5 HELIX 16 16 ALA A 239 GLY A 242 5 4 HELIX 17 17 PRO A 265 TYR A 269 5 5 HELIX 18 18 ARG A 329 MET A 333 5 5 HELIX 19 19 ASP A 387 LYS A 392 1 6 HELIX 20 20 TYR A 393 LEU A 397 5 5 SHEET 1 AA 5 GLY A 87 TYR A 91 0 SHEET 2 AA 5 PRO A 97 ILE A 102 -1 O VAL A 98 N CYS A 89 SHEET 3 AA 5 ILE A 149 ASP A 154 1 O VAL A 150 N TRP A 99 SHEET 4 AA 5 LEU A 186 VAL A 192 1 N LYS A 187 O ILE A 149 SHEET 5 AA 5 ILE A 217 VAL A 219 1 O ILE A 218 N ILE A 191 SHEET 1 AB 4 HIS A 280 ASN A 285 0 SHEET 2 AB 4 ALA A 374 LEU A 384 -1 O LYS A 375 N ILE A 284 SHEET 3 AB 4 VAL A 302 SER A 308 -1 O VAL A 302 N LEU A 384 SHEET 4 AB 4 GLU A 349 THR A 354 -1 O GLU A 349 N PHE A 307 SHEET 1 AC 4 SER A 289 ILE A 296 0 SHEET 2 AC 4 GLY A 359 ASP A 366 -1 O GLY A 359 N ILE A 296 SHEET 3 AC 4 ILE A 314 LYS A 321 -1 O GLY A 315 N ASP A 366 SHEET 4 AC 4 THR A 334 TYR A 342 -1 O THR A 334 N LEU A 320 SITE 1 AC1 4 LYS A 193 TRP A 224 GLN A 240 HOH A2324 SITE 1 AC2 4 ARG A 304 GLN A 306 GLU A 382 HOH A2265 SITE 1 AC3 6 THR A 246 ASP A 247 PRO A 248 THR A 256 SITE 2 AC3 6 LYS A 257 HOH A2491 SITE 1 AC4 5 LEU A 88 GLY A 90 TYR A 91 GLU A 134 SITE 2 AC4 5 LYS A 257 SITE 1 AC5 4 ARG A 93 PRO A 234 HOH A2188 HOH A2492 SITE 1 AC6 8 PRO A 31 ARG A 63 ASP A 69 ASN A 285 SITE 2 AC6 8 ARG A 286 GLY A 287 SER A 288 HOH A2138 CRYST1 83.243 83.243 174.363 90.00 90.00 90.00 P 41 21 2 8 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 0.012013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005735 0.00000