HEADER LIGASE 13-MAR-17 5V58 TITLE CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE IN COMPLEX WITH AZE- TITLE 2 SA COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BIFUNCTIONAL AMINOACYL-TRNA SYNTHETASE, CELL PROLIFERATION- COMPND 5 INDUCING GENE 32 PROTEIN, GLUTAMATYL-PROLYL-TRNA SYNTHETASE; COMPND 6 EC: 6.1.1.17, 6.1.1.15; COMPND 7 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: EPRS, GLNS, PARS, QARS, QPRS, PIG32; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE, AMINOACYL-TRNA SYNTHETASE, NON-PROTEINOGENIC AMINO ACIDS EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHOU,Y.SONG,P.SCHIMMEL REVDAT 4 20-NOV-24 5V58 1 REMARK REVDAT 3 04-OCT-23 5V58 1 REMARK REVDAT 2 01-JAN-20 5V58 1 REMARK REVDAT 1 10-JAN-18 5V58 0 JRNL AUTH Y.SONG,H.ZHOU,M.N.VO,Y.SHI,M.H.NAWAZ,O.VARGAS-RODRIGUEZ, JRNL AUTH 2 J.K.DIEDRICH,J.R.YATES,S.KISHI,K.MUSIER-FORSYTH,P.SCHIMMEL JRNL TITL DOUBLE MIMICRY EVADES TRNA SYNTHETASE EDITING BY TOXIC JRNL TITL 2 VEGETABLE-SOURCED NON-PROTEINOGENIC AMINO ACID. JRNL REF NAT COMMUN V. 8 2281 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29273753 JRNL DOI 10.1038/S41467-017-02201-Z REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 13977 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 749 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) : 2.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 931 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3741 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.33000 REMARK 3 B22 (A**2) : -1.33000 REMARK 3 B33 (A**2) : 4.30000 REMARK 3 B12 (A**2) : -1.33000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.378 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.257 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.639 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3868 ; 0.004 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3604 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5257 ; 1.045 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8276 ; 0.695 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 5.160 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;33.340 ;24.023 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 638 ;13.108 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;10.846 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 583 ; 0.050 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4347 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 885 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 REMARK 4 REMARK 4 5V58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14793 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.590 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4HVC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG3350, 250 MM SODIUM NITRATE, 100 REMARK 280 MM 3-(1-PYRIDINO)-1-PROPANE SULFONATE, EVAPORATION, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 72.51533 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 36.25767 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 36.25767 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 72.51533 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -104.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -36.25767 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 MET A 994 REMARK 465 HIS A 995 REMARK 465 HIS A 996 REMARK 465 HIS A 997 REMARK 465 HIS A 998 REMARK 465 HIS A 999 REMARK 465 HIS A 1000 REMARK 465 GLY A 1001 REMARK 465 SER A 1002 REMARK 465 GLY A 1003 REMARK 465 GLU A 1004 REMARK 465 GLY A 1005 REMARK 465 GLN A 1006 REMARK 465 GLY A 1007 REMARK 465 PRO A 1008 REMARK 465 LYS A 1009 REMARK 465 LYS A 1010 REMARK 465 GLN A 1011 REMARK 465 THR A 1012 REMARK 465 THR A 1092 REMARK 465 HIS A 1093 REMARK 465 VAL A 1094 REMARK 465 ALA A 1095 REMARK 465 ASP A 1096 REMARK 465 PHE A 1097 REMARK 465 GLY A 1310 REMARK 465 ILE A 1311 REMARK 465 THR A 1312 REMARK 465 ASN A 1313 REMARK 465 ALA A 1314 REMARK 465 LEU A 1315 REMARK 465 GLN A 1465 REMARK 465 ASP A 1466 REMARK 465 LEU A 1467 REMARK 465 GLU A 1468 REMARK 465 PRO A 1469 REMARK 465 GLY A 1470 REMARK 465 ALA A 1471 REMARK 465 PRO A 1472 REMARK 465 SER A 1473 REMARK 465 GLN A 1490 REMARK 465 PRO A 1491 REMARK 465 GLY A 1492 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 LYS A1034 CG CD CE NZ REMARK 470 LYS A1089 CE NZ REMARK 470 GLU A1090 CG CD OE1 OE2 REMARK 470 LYS A1091 CG CD CE NZ REMARK 470 GLU A1100 CG CD OE1 OE2 REMARK 470 LYS A1109 CG CD CE NZ REMARK 470 LYS A1132 CG CD CE NZ REMARK 470 PHE A1155 CG CD1 CD2 CE1 CE2 CZ REMARK 470 HIS A1157 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A1260 CG CD CE NZ REMARK 470 SER A1316 OG REMARK 470 GLU A1318 CG CD OE1 OE2 REMARK 470 ASP A1319 CG OD1 OD2 REMARK 470 LYS A1320 CG CD CE NZ REMARK 470 ARG A1372 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1375 CG CD CE NZ REMARK 470 LYS A1400 CD CE NZ REMARK 470 ARG A1463 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1477 CG CD CE NZ REMARK 470 LYS A1484 CE NZ REMARK 470 LYS A1494 CG CD CE NZ REMARK 470 LYS A1499 CG CD CE NZ REMARK 470 LYS A1503 CD CE NZ 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 PHE A1155 41.68 -87.69 REMARK 500 LYS A1156 -154.84 -92.38 REMARK 500 PHE A1161 -56.57 66.81 REMARK 500 LYS A1484 79.76 -114.57 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 ZN A1602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1448 SG REMARK 620 2 CYS A1495 SG 96.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8X1 A 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5V59 RELATED DB: PDB DBREF 5V58 A 1003 1512 UNP P07814 SYEP_HUMAN 1003 1512 SEQADV 5V58 MET A 994 UNP P07814 EXPRESSION TAG SEQADV 5V58 HIS A 995 UNP P07814 EXPRESSION TAG SEQADV 5V58 HIS A 996 UNP P07814 EXPRESSION TAG SEQADV 5V58 HIS A 997 UNP P07814 EXPRESSION TAG SEQADV 5V58 HIS A 998 UNP P07814 EXPRESSION TAG SEQADV 5V58 HIS A 999 UNP P07814 EXPRESSION TAG SEQADV 5V58 HIS A 1000 UNP P07814 EXPRESSION TAG SEQADV 5V58 GLY A 1001 UNP P07814 EXPRESSION TAG SEQADV 5V58 SER A 1002 UNP P07814 EXPRESSION TAG SEQRES 1 A 519 MET HIS HIS HIS HIS HIS HIS GLY SER GLY GLU GLY GLN SEQRES 2 A 519 GLY PRO LYS LYS GLN THR ARG LEU GLY LEU GLU ALA LYS SEQRES 3 A 519 LYS GLU GLU ASN LEU ALA ASP TRP TYR SER GLN VAL ILE SEQRES 4 A 519 THR LYS SER GLU MET ILE GLU TYR HIS ASP ILE SER GLY SEQRES 5 A 519 CYS TYR ILE LEU ARG PRO TRP ALA TYR ALA ILE TRP GLU SEQRES 6 A 519 ALA ILE LYS ASP PHE PHE ASP ALA GLU ILE LYS LYS LEU SEQRES 7 A 519 GLY VAL GLU ASN CYS TYR PHE PRO MET PHE VAL SER GLN SEQRES 8 A 519 SER ALA LEU GLU LYS GLU LYS THR HIS VAL ALA ASP PHE SEQRES 9 A 519 ALA PRO GLU VAL ALA TRP VAL THR ARG SER GLY LYS THR SEQRES 10 A 519 GLU LEU ALA GLU PRO ILE ALA ILE ARG PRO THR SER GLU SEQRES 11 A 519 THR VAL MET TYR PRO ALA TYR ALA LYS TRP VAL GLN SER SEQRES 12 A 519 HIS ARG ASP LEU PRO ILE LYS LEU ASN GLN TRP CYS ASN SEQRES 13 A 519 VAL VAL ARG TRP GLU PHE LYS HIS PRO GLN PRO PHE LEU SEQRES 14 A 519 ARG THR ARG GLU PHE LEU TRP GLN GLU GLY HIS SER ALA SEQRES 15 A 519 PHE ALA THR MET GLU GLU ALA ALA GLU GLU VAL LEU GLN SEQRES 16 A 519 ILE LEU ASP LEU TYR ALA GLN VAL TYR GLU GLU LEU LEU SEQRES 17 A 519 ALA ILE PRO VAL VAL LYS GLY ARG LYS THR GLU LYS GLU SEQRES 18 A 519 LYS PHE ALA GLY GLY ASP TYR THR THR THR ILE GLU ALA SEQRES 19 A 519 PHE ILE SER ALA SER GLY ARG ALA ILE GLN GLY GLY THR SEQRES 20 A 519 SER HIS HIS LEU GLY GLN ASN PHE SER LYS MET PHE GLU SEQRES 21 A 519 ILE VAL PHE GLU ASP PRO LYS ILE PRO GLY GLU LYS GLN SEQRES 22 A 519 PHE ALA TYR GLN ASN SER TRP GLY LEU THR THR ARG THR SEQRES 23 A 519 ILE GLY VAL MET THR MET VAL HIS GLY ASP ASN MET GLY SEQRES 24 A 519 LEU VAL LEU PRO PRO ARG VAL ALA CYS VAL GLN VAL VAL SEQRES 25 A 519 ILE ILE PRO CYS GLY ILE THR ASN ALA LEU SER GLU GLU SEQRES 26 A 519 ASP LYS GLU ALA LEU ILE ALA LYS CYS ASN ASP TYR ARG SEQRES 27 A 519 ARG ARG LEU LEU SER VAL ASN ILE ARG VAL ARG ALA ASP SEQRES 28 A 519 LEU ARG ASP ASN TYR SER PRO GLY TRP LYS PHE ASN HIS SEQRES 29 A 519 TRP GLU LEU LYS GLY VAL PRO ILE ARG LEU GLU VAL GLY SEQRES 30 A 519 PRO ARG ASP MET LYS SER CYS GLN PHE VAL ALA VAL ARG SEQRES 31 A 519 ARG ASP THR GLY GLU LYS LEU THR VAL ALA GLU ASN GLU SEQRES 32 A 519 ALA GLU THR LYS LEU GLN ALA ILE LEU GLU ASP ILE GLN SEQRES 33 A 519 VAL THR LEU PHE THR ARG ALA SER GLU ASP LEU LYS THR SEQRES 34 A 519 HIS MET VAL VAL ALA ASN THR MET GLU ASP PHE GLN LYS SEQRES 35 A 519 ILE LEU ASP SER GLY LYS ILE VAL GLN ILE PRO PHE CYS SEQRES 36 A 519 GLY GLU ILE ASP CYS GLU ASP TRP ILE LYS LYS THR THR SEQRES 37 A 519 ALA ARG ASP GLN ASP LEU GLU PRO GLY ALA PRO SER MET SEQRES 38 A 519 GLY ALA LYS SER LEU CYS ILE PRO PHE LYS PRO LEU CYS SEQRES 39 A 519 GLU LEU GLN PRO GLY ALA LYS CYS VAL CYS GLY LYS ASN SEQRES 40 A 519 PRO ALA LYS TYR TYR THR LEU PHE GLY ARG SER TYR HET 8X1 A1601 29 HET ZN A1602 1 HETNAM 8X1 5'-O-{[(2S)-AZETIDINE-2-CARBONYL]SULFAMOYL}ADENOSINE HETNAM ZN ZINC ION FORMUL 2 8X1 C14 H19 N7 O7 S FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *26(H2 O) HELIX 1 AA1 ASN A 1023 SER A 1035 1 13 HELIX 2 AA2 ARG A 1050 LEU A 1071 1 22 HELIX 3 AA3 SER A 1083 LYS A 1091 1 9 HELIX 4 AA4 SER A 1122 VAL A 1134 1 13 HELIX 5 AA5 SER A 1136 LEU A 1140 5 5 HELIX 6 AA6 THR A 1178 GLU A 1199 1 22 HELIX 7 AA7 GLN A 1246 PHE A 1252 1 7 HELIX 8 AA8 THR A 1277 GLY A 1288 1 12 HELIX 9 AA9 GLU A 1317 SER A 1336 1 20 HELIX 10 AB1 SER A 1350 GLY A 1362 1 13 HELIX 11 AB2 GLY A 1370 SER A 1376 1 7 HELIX 12 AB3 GLU A 1396 HIS A 1423 1 28 HELIX 13 AB4 THR A 1429 SER A 1439 1 11 HELIX 14 AB5 GLU A 1450 ASP A 1464 1 15 SHEET 1 AA1 2 ILE A1038 TYR A1040 0 SHEET 2 AA1 2 TYR A1047 LEU A1049 -1 O ILE A1048 N GLU A1039 SHEET 1 AA211 GLU A1074 ASN A1075 0 SHEET 2 AA211 ILE A1142 VAL A1151 1 O LYS A1143 N GLU A1074 SHEET 3 AA211 GLU A1166 PHE A1176 -1 O HIS A1173 N LEU A1144 SHEET 4 AA211 TYR A1269 THR A1276 -1 O TYR A1269 N PHE A1176 SHEET 5 AA211 ARG A1234 GLY A1245 -1 N HIS A1242 O SER A1272 SHEET 6 AA211 TYR A1221 ILE A1229 -1 N TYR A1221 O HIS A1243 SHEET 7 AA211 VAL A1206 ARG A1209 -1 N GLY A1208 O THR A1224 SHEET 8 AA211 LYS A1477 PRO A1482 -1 O ILE A1481 N ARG A1209 SHEET 9 AA211 TYR A1504 GLY A1509 -1 O LEU A1507 N LEU A1479 SHEET 10 AA211 ILE A1442 PHE A1447 -1 N VAL A1443 O PHE A1508 SHEET 11 AA211 MET A1424 VAL A1426 1 N VAL A1425 O GLN A1444 SHEET 1 AA3 3 PHE A1081 VAL A1082 0 SHEET 2 AA3 3 THR A1110 ILE A1118 -1 O ALA A1117 N VAL A1082 SHEET 3 AA3 3 TRP A1103 SER A1107 -1 N VAL A1104 O ILE A1116 SHEET 1 AA4 2 VAL A1255 GLU A1257 0 SHEET 2 AA4 2 LYS A1265 PHE A1267 -1 O GLN A1266 N PHE A1256 SHEET 1 AA5 5 VAL A1341 ALA A1343 0 SHEET 2 AA5 5 VAL A1304 PRO A1308 1 N ILE A1306 O ARG A1342 SHEET 3 AA5 5 ILE A1365 VAL A1369 1 O LEU A1367 N ILE A1307 SHEET 4 AA5 5 GLN A1378 ARG A1383 -1 O VAL A1380 N GLU A1368 SHEET 5 AA5 5 LYS A1389 ALA A1393 -1 O LEU A1390 N ALA A1381 SSBOND 1 CYS A 1453 CYS A 1497 1555 1555 2.03 LINK SG CYS A1448 ZN ZN A1602 1555 1555 2.56 LINK SG CYS A1495 ZN ZN A1602 1555 1555 2.62 CISPEP 1 LEU A 1140 PRO A 1141 0 2.27 SITE 1 AC1 16 THR A1121 GLU A1123 ARG A1152 GLU A1154 SITE 2 AC1 16 PHE A1161 LEU A1162 THR A1164 PHE A1167 SITE 3 AC1 16 TRP A1169 GLN A1237 GLY A1239 THR A1240 SITE 4 AC1 16 HIS A1242 GLY A1274 THR A1276 ARG A1278 SITE 1 AC2 5 CYS A1448 CYS A1453 CYS A1495 CYS A1497 SITE 2 AC2 5 ASN A1500 CRYST1 86.766 86.766 108.773 90.00 90.00 120.00 P 32 2 1 6 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 0.011525 0.006654 0.000000 0.00000 SCALE2 0.000000 0.013308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009193 0.00000