HEADER LIGASE 18-JAN-17 5UJJ TITLE CRYSTAL STRUCTURE OF HUMAN H130R TRYPTOPHANYL-TRNA SYNTHETASE IN TITLE 2 COMPLEX WITH TRPAMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHAN--TRNA LIGASE, CYTOPLASMIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: INTERFERON-INDUCED PROTEIN 53,IFP53,TRYPTOPHANYL-TRNA COMPND 5 SYNTHETASE,HWRS; COMPND 6 EC: 6.1.1.2; 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: WARS, IFI53, WRS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET20B KEYWDS ROSSMANN-FOLD CATALYTIC DOMAIN, ANTI-CODON BINDING DOMAIN, H130R KEYWDS 2 MUTATION, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR X.XU,X.-L.YANG REVDAT 3 04-OCT-23 5UJJ 1 REMARK LINK REVDAT 2 29-AUG-18 5UJJ 1 JRNL REVDAT 1 17-JAN-18 5UJJ 0 JRNL AUTH X.XU,H.ZHOU,Q.ZHOU,F.HONG,M.N.VO,W.NIU,Z.WANG,X.XIONG, JRNL AUTH 2 K.NAKAMURA,K.WAKASUGI,P.SCHIMMEL,X.L.YANG JRNL TITL AN ALTERNATIVE CONFORMATION OF HUMAN TRPRS SUGGESTS A ROLE JRNL TITL 2 OF ZINC IN ACTIVATING NON-ENZYMATIC FUNCTION. JRNL REF RNA BIOL V. 15 649 2018 JRNL REFN ESSN 1555-8584 JRNL PMID 28910573 JRNL DOI 10.1080/15476286.2017.1377868 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 53339 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2735 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3898 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 209 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6702 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : -0.43000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.241 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.179 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.422 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6950 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6543 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9390 ; 1.113 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15087 ; 0.876 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 832 ; 5.817 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;31.170 ;24.036 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1213 ;13.249 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;11.755 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1011 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7795 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1656 ; 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5UJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 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 : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56074 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 75.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : 0.15900 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: PHASER REMARK 200 STARTING MODEL: 2QUI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG1500, 0.1MOL/L BIS-TRIS PH6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 68.17600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.63850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.17600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 47.63850 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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 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 1 REMARK 465 PRO A 2 REMARK 465 ASN A 3 REMARK 465 SER A 4 REMARK 465 GLU A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 7 REMARK 465 GLY A 65 REMARK 465 ASN A 66 REMARK 465 PRO A 67 REMARK 465 ALA A 68 REMARK 465 PRO A 69 REMARK 465 THR A 70 REMARK 465 SER A 71 REMARK 465 ASN A 72 REMARK 465 HIS A 73 REMARK 465 GLY A 74 REMARK 465 PRO A 75 REMARK 465 ASP A 76 REMARK 465 ALA A 77 REMARK 465 THR A 78 REMARK 465 GLU A 79 REMARK 465 ALA A 80 REMARK 465 GLU A 81 REMARK 465 GLN A 471 REMARK 465 LYS A 472 REMARK 465 LEU A 473 REMARK 465 ALA A 474 REMARK 465 ALA A 475 REMARK 465 ALA A 476 REMARK 465 LEU A 477 REMARK 465 GLU A 478 REMARK 465 HIS A 479 REMARK 465 HIS A 480 REMARK 465 HIS A 481 REMARK 465 HIS A 482 REMARK 465 HIS A 483 REMARK 465 HIS A 484 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 ASN B 3 REMARK 465 SER B 4 REMARK 465 GLU B 5 REMARK 465 PRO B 6 REMARK 465 ALA B 7 REMARK 465 SER B 8 REMARK 465 LEU B 9 REMARK 465 LEU B 10 REMARK 465 GLU B 11 REMARK 465 LEU B 12 REMARK 465 PHE B 13 REMARK 465 ASN B 14 REMARK 465 SER B 15 REMARK 465 ILE B 16 REMARK 465 ALA B 17 REMARK 465 THR B 18 REMARK 465 GLN B 19 REMARK 465 GLY B 20 REMARK 465 GLU B 21 REMARK 465 LEU B 22 REMARK 465 VAL B 23 REMARK 465 ARG B 24 REMARK 465 SER B 25 REMARK 465 LEU B 26 REMARK 465 LYS B 27 REMARK 465 ALA B 28 REMARK 465 GLY B 29 REMARK 465 ASN B 30 REMARK 465 ALA B 31 REMARK 465 SER B 32 REMARK 465 LYS B 33 REMARK 465 ASP B 34 REMARK 465 GLU B 35 REMARK 465 ILE B 36 REMARK 465 ASP B 37 REMARK 465 SER B 38 REMARK 465 ALA B 39 REMARK 465 VAL B 40 REMARK 465 LYS B 41 REMARK 465 MET B 42 REMARK 465 LEU B 43 REMARK 465 VAL B 44 REMARK 465 SER B 45 REMARK 465 LEU B 46 REMARK 465 LYS B 47 REMARK 465 MET B 48 REMARK 465 SER B 49 REMARK 465 TYR B 50 REMARK 465 LYS B 51 REMARK 465 ALA B 52 REMARK 465 ALA B 53 REMARK 465 ALA B 54 REMARK 465 GLY B 55 REMARK 465 GLU B 56 REMARK 465 ASP B 57 REMARK 465 TYR B 58 REMARK 465 LYS B 59 REMARK 465 ALA B 60 REMARK 465 ASP B 61 REMARK 465 CYS B 62 REMARK 465 PRO B 63 REMARK 465 PRO B 64 REMARK 465 GLY B 65 REMARK 465 ASN B 66 REMARK 465 PRO B 67 REMARK 465 ALA B 68 REMARK 465 PRO B 69 REMARK 465 THR B 70 REMARK 465 SER B 71 REMARK 465 ASN B 72 REMARK 465 HIS B 73 REMARK 465 GLY B 74 REMARK 465 PRO B 75 REMARK 465 ASP B 76 REMARK 465 ALA B 77 REMARK 465 THR B 78 REMARK 465 GLU B 79 REMARK 465 ALA B 80 REMARK 465 GLU B 81 REMARK 465 GLU B 82 REMARK 465 GLN B 471 REMARK 465 LYS B 472 REMARK 465 LEU B 473 REMARK 465 ALA B 474 REMARK 465 ALA B 475 REMARK 465 ALA B 476 REMARK 465 LEU B 477 REMARK 465 GLU B 478 REMARK 465 HIS B 479 REMARK 465 HIS B 480 REMARK 465 HIS B 481 REMARK 465 HIS B 482 REMARK 465 HIS B 483 REMARK 465 HIS B 484 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 PHE B 390 CG CD1 CD2 CE1 CE2 CZ 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 30 32.92 -95.79 REMARK 500 ALA A 168 102.69 69.85 REMARK 500 PHE B 293 76.92 -117.34 REMARK 500 ARG B 298 -126.93 53.16 REMARK 500 THR B 383 143.38 73.26 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 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 163 O REMARK 620 2 SER A 165 OG 72.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYM A 501 O1P REMARK 620 2 HOH A 635 O 80.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 312 OD1 REMARK 620 2 TYM B 501 O2P 147.6 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 TYM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TYM B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UJI RELATED DB: PDB DBREF 5UJJ A 1 471 UNP P23381 SYWC_HUMAN 1 471 DBREF 5UJJ B 1 471 UNP P23381 SYWC_HUMAN 1 471 SEQADV 5UJJ ARG A 130 UNP P23381 HIS 130 ENGINEERED MUTATION SEQADV 5UJJ LYS A 472 UNP P23381 EXPRESSION TAG SEQADV 5UJJ LEU A 473 UNP P23381 EXPRESSION TAG SEQADV 5UJJ ALA A 474 UNP P23381 EXPRESSION TAG SEQADV 5UJJ ALA A 475 UNP P23381 EXPRESSION TAG SEQADV 5UJJ ALA A 476 UNP P23381 EXPRESSION TAG SEQADV 5UJJ LEU A 477 UNP P23381 EXPRESSION TAG SEQADV 5UJJ GLU A 478 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS A 479 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS A 480 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS A 481 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS A 482 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS A 483 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS A 484 UNP P23381 EXPRESSION TAG SEQADV 5UJJ ARG B 130 UNP P23381 HIS 130 ENGINEERED MUTATION SEQADV 5UJJ LYS B 472 UNP P23381 EXPRESSION TAG SEQADV 5UJJ LEU B 473 UNP P23381 EXPRESSION TAG SEQADV 5UJJ ALA B 474 UNP P23381 EXPRESSION TAG SEQADV 5UJJ ALA B 475 UNP P23381 EXPRESSION TAG SEQADV 5UJJ ALA B 476 UNP P23381 EXPRESSION TAG SEQADV 5UJJ LEU B 477 UNP P23381 EXPRESSION TAG SEQADV 5UJJ GLU B 478 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS B 479 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS B 480 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS B 481 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS B 482 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS B 483 UNP P23381 EXPRESSION TAG SEQADV 5UJJ HIS B 484 UNP P23381 EXPRESSION TAG SEQRES 1 A 484 MET PRO ASN SER GLU PRO ALA SER LEU LEU GLU LEU PHE SEQRES 2 A 484 ASN SER ILE ALA THR GLN GLY GLU LEU VAL ARG SER LEU SEQRES 3 A 484 LYS ALA GLY ASN ALA SER LYS ASP GLU ILE ASP SER ALA SEQRES 4 A 484 VAL LYS MET LEU VAL SER LEU LYS MET SER TYR LYS ALA SEQRES 5 A 484 ALA ALA GLY GLU ASP TYR LYS ALA ASP CYS PRO PRO GLY SEQRES 6 A 484 ASN PRO ALA PRO THR SER ASN HIS GLY PRO ASP ALA THR SEQRES 7 A 484 GLU ALA GLU GLU ASP PHE VAL ASP PRO TRP THR VAL GLN SEQRES 8 A 484 THR SER SER ALA LYS GLY ILE ASP TYR ASP LYS LEU ILE SEQRES 9 A 484 VAL ARG PHE GLY SER SER LYS ILE ASP LYS GLU LEU ILE SEQRES 10 A 484 ASN ARG ILE GLU ARG ALA THR GLY GLN ARG PRO HIS ARG SEQRES 11 A 484 PHE LEU ARG ARG GLY ILE PHE PHE SER HIS ARG ASP MET SEQRES 12 A 484 ASN GLN VAL LEU ASP ALA TYR GLU ASN LYS LYS PRO PHE SEQRES 13 A 484 TYR LEU TYR THR GLY ARG GLY PRO SER SER GLU ALA MET SEQRES 14 A 484 HIS VAL GLY HIS LEU ILE PRO PHE ILE PHE THR LYS TRP SEQRES 15 A 484 LEU GLN ASP VAL PHE ASN VAL PRO LEU VAL ILE GLN MET SEQRES 16 A 484 THR ASP ASP GLU LYS TYR LEU TRP LYS ASP LEU THR LEU SEQRES 17 A 484 ASP GLN ALA TYR SER TYR ALA VAL GLU ASN ALA LYS ASP SEQRES 18 A 484 ILE ILE ALA CYS GLY PHE ASP ILE ASN LYS THR PHE ILE SEQRES 19 A 484 PHE SER ASP LEU ASP TYR MET GLY MET SER SER GLY PHE SEQRES 20 A 484 TYR LYS ASN VAL VAL LYS ILE GLN LYS HIS VAL THR PHE SEQRES 21 A 484 ASN GLN VAL LYS GLY ILE PHE GLY PHE THR ASP SER ASP SEQRES 22 A 484 CYS ILE GLY LYS ILE SER PHE PRO ALA ILE GLN ALA ALA SEQRES 23 A 484 PRO SER PHE SER ASN SER PHE PRO GLN ILE PHE ARG ASP SEQRES 24 A 484 ARG THR ASP ILE GLN CYS LEU ILE PRO CYS ALA ILE ASP SEQRES 25 A 484 GLN ASP PRO TYR PHE ARG MET THR ARG ASP VAL ALA PRO SEQRES 26 A 484 ARG ILE GLY TYR PRO LYS PRO ALA LEU LEU HIS SER THR SEQRES 27 A 484 PHE PHE PRO ALA LEU GLN GLY ALA GLN THR LYS MET SER SEQRES 28 A 484 ALA SER ASP PRO ASN SER SER ILE PHE LEU THR ASP THR SEQRES 29 A 484 ALA LYS GLN ILE LYS THR LYS VAL ASN LYS HIS ALA PHE SEQRES 30 A 484 SER GLY GLY ARG ASP THR ILE GLU GLU HIS ARG GLN PHE SEQRES 31 A 484 GLY GLY ASN CYS ASP VAL ASP VAL SER PHE MET TYR LEU SEQRES 32 A 484 THR PHE PHE LEU GLU ASP ASP ASP LYS LEU GLU GLN ILE SEQRES 33 A 484 ARG LYS ASP TYR THR SER GLY ALA MET LEU THR GLY GLU SEQRES 34 A 484 LEU LYS LYS ALA LEU ILE GLU VAL LEU GLN PRO LEU ILE SEQRES 35 A 484 ALA GLU HIS GLN ALA ARG ARG LYS GLU VAL THR ASP GLU SEQRES 36 A 484 ILE VAL LYS GLU PHE MET THR PRO ARG LYS LEU SER PHE SEQRES 37 A 484 ASP PHE GLN LYS LEU ALA ALA ALA LEU GLU HIS HIS HIS SEQRES 38 A 484 HIS HIS HIS SEQRES 1 B 484 MET PRO ASN SER GLU PRO ALA SER LEU LEU GLU LEU PHE SEQRES 2 B 484 ASN SER ILE ALA THR GLN GLY GLU LEU VAL ARG SER LEU SEQRES 3 B 484 LYS ALA GLY ASN ALA SER LYS ASP GLU ILE ASP SER ALA SEQRES 4 B 484 VAL LYS MET LEU VAL SER LEU LYS MET SER TYR LYS ALA SEQRES 5 B 484 ALA ALA GLY GLU ASP TYR LYS ALA ASP CYS PRO PRO GLY SEQRES 6 B 484 ASN PRO ALA PRO THR SER ASN HIS GLY PRO ASP ALA THR SEQRES 7 B 484 GLU ALA GLU GLU ASP PHE VAL ASP PRO TRP THR VAL GLN SEQRES 8 B 484 THR SER SER ALA LYS GLY ILE ASP TYR ASP LYS LEU ILE SEQRES 9 B 484 VAL ARG PHE GLY SER SER LYS ILE ASP LYS GLU LEU ILE SEQRES 10 B 484 ASN ARG ILE GLU ARG ALA THR GLY GLN ARG PRO HIS ARG SEQRES 11 B 484 PHE LEU ARG ARG GLY ILE PHE PHE SER HIS ARG ASP MET SEQRES 12 B 484 ASN GLN VAL LEU ASP ALA TYR GLU ASN LYS LYS PRO PHE SEQRES 13 B 484 TYR LEU TYR THR GLY ARG GLY PRO SER SER GLU ALA MET SEQRES 14 B 484 HIS VAL GLY HIS LEU ILE PRO PHE ILE PHE THR LYS TRP SEQRES 15 B 484 LEU GLN ASP VAL PHE ASN VAL PRO LEU VAL ILE GLN MET SEQRES 16 B 484 THR ASP ASP GLU LYS TYR LEU TRP LYS ASP LEU THR LEU SEQRES 17 B 484 ASP GLN ALA TYR SER TYR ALA VAL GLU ASN ALA LYS ASP SEQRES 18 B 484 ILE ILE ALA CYS GLY PHE ASP ILE ASN LYS THR PHE ILE SEQRES 19 B 484 PHE SER ASP LEU ASP TYR MET GLY MET SER SER GLY PHE SEQRES 20 B 484 TYR LYS ASN VAL VAL LYS ILE GLN LYS HIS VAL THR PHE SEQRES 21 B 484 ASN GLN VAL LYS GLY ILE PHE GLY PHE THR ASP SER ASP SEQRES 22 B 484 CYS ILE GLY LYS ILE SER PHE PRO ALA ILE GLN ALA ALA SEQRES 23 B 484 PRO SER PHE SER ASN SER PHE PRO GLN ILE PHE ARG ASP SEQRES 24 B 484 ARG THR ASP ILE GLN CYS LEU ILE PRO CYS ALA ILE ASP SEQRES 25 B 484 GLN ASP PRO TYR PHE ARG MET THR ARG ASP VAL ALA PRO SEQRES 26 B 484 ARG ILE GLY TYR PRO LYS PRO ALA LEU LEU HIS SER THR SEQRES 27 B 484 PHE PHE PRO ALA LEU GLN GLY ALA GLN THR LYS MET SER SEQRES 28 B 484 ALA SER ASP PRO ASN SER SER ILE PHE LEU THR ASP THR SEQRES 29 B 484 ALA LYS GLN ILE LYS THR LYS VAL ASN LYS HIS ALA PHE SEQRES 30 B 484 SER GLY GLY ARG ASP THR ILE GLU GLU HIS ARG GLN PHE SEQRES 31 B 484 GLY GLY ASN CYS ASP VAL ASP VAL SER PHE MET TYR LEU SEQRES 32 B 484 THR PHE PHE LEU GLU ASP ASP ASP LYS LEU GLU GLN ILE SEQRES 33 B 484 ARG LYS ASP TYR THR SER GLY ALA MET LEU THR GLY GLU SEQRES 34 B 484 LEU LYS LYS ALA LEU ILE GLU VAL LEU GLN PRO LEU ILE SEQRES 35 B 484 ALA GLU HIS GLN ALA ARG ARG LYS GLU VAL THR ASP GLU SEQRES 36 B 484 ILE VAL LYS GLU PHE MET THR PRO ARG LYS LEU SER PHE SEQRES 37 B 484 ASP PHE GLN LYS LEU ALA ALA ALA LEU GLU HIS HIS HIS SEQRES 38 B 484 HIS HIS HIS HET TYM A 501 37 HET MG A 502 1 HET MG A 503 1 HET TYM B 501 37 HET MG B 502 1 HETNAM TYM TRYPTOPHANYL-5'AMP HETNAM MG MAGNESIUM ION FORMUL 3 TYM 2(C21 H24 N7 O8 P) FORMUL 4 MG 3(MG 2+) FORMUL 8 HOH *162(H2 O) HELIX 1 AA1 SER A 8 GLY A 29 1 22 HELIX 2 AA2 SER A 32 GLY A 55 1 24 HELIX 3 AA3 ASP A 99 GLY A 108 1 10 HELIX 4 AA4 ASP A 113 GLY A 125 1 13 HELIX 5 AA5 HIS A 129 ARG A 134 1 6 HELIX 6 AA6 ASP A 142 ASN A 152 1 11 HELIX 7 AA7 HIS A 170 GLY A 172 5 3 HELIX 8 AA8 HIS A 173 ASN A 188 1 16 HELIX 9 AA9 THR A 196 LYS A 204 1 9 HELIX 10 AB1 THR A 207 ALA A 224 1 18 HELIX 11 AB2 ASP A 237 GLY A 242 1 6 HELIX 12 AB3 GLY A 246 HIS A 257 1 12 HELIX 13 AB4 THR A 259 GLY A 268 1 10 HELIX 14 AB5 CYS A 274 PHE A 280 1 7 HELIX 15 AB6 PHE A 280 ALA A 286 1 7 HELIX 16 AB7 PRO A 287 SER A 292 5 6 HELIX 17 AB8 PHE A 293 ARG A 298 1 6 HELIX 18 AB9 GLN A 313 ALA A 324 1 12 HELIX 19 AC1 PRO A 325 GLY A 328 5 4 HELIX 20 AC2 THR A 364 ALA A 376 1 13 HELIX 21 AC3 THR A 383 GLY A 391 1 9 HELIX 22 AC4 ASP A 397 LEU A 407 1 11 HELIX 23 AC5 ASP A 409 GLY A 423 1 15 HELIX 24 AC6 LEU A 426 VAL A 452 1 27 HELIX 25 AC7 THR A 453 THR A 462 1 10 HELIX 26 AC8 ASP B 99 GLY B 108 1 10 HELIX 27 AC9 ASP B 113 GLY B 125 1 13 HELIX 28 AD1 HIS B 129 ARG B 134 1 6 HELIX 29 AD2 ASP B 142 ASN B 152 1 11 HELIX 30 AD3 HIS B 173 ASN B 188 1 16 HELIX 31 AD4 THR B 196 LYS B 204 1 9 HELIX 32 AD5 THR B 207 ALA B 224 1 18 HELIX 33 AD6 ASP B 237 MET B 241 1 5 HELIX 34 AD7 GLY B 242 SER B 244 5 3 HELIX 35 AD8 GLY B 246 HIS B 257 1 12 HELIX 36 AD9 THR B 259 GLY B 268 1 10 HELIX 37 AE1 CYS B 274 ALA B 286 1 13 HELIX 38 AE2 PRO B 287 SER B 292 5 6 HELIX 39 AE3 PHE B 293 ARG B 298 1 6 HELIX 40 AE4 GLN B 313 ILE B 327 1 15 HELIX 41 AE5 ASP B 354 SER B 358 5 5 HELIX 42 AE6 THR B 364 HIS B 375 1 12 HELIX 43 AE7 THR B 383 GLY B 391 1 9 HELIX 44 AE8 ASP B 397 LEU B 407 1 11 HELIX 45 AE9 ASP B 409 GLY B 423 1 15 HELIX 46 AF1 LEU B 426 GLU B 451 1 26 HELIX 47 AF2 THR B 453 MET B 461 1 9 SHEET 1 AA1 2 PHE A 84 VAL A 85 0 SHEET 2 AA1 2 VAL A 90 GLN A 91 -1 O GLN A 91 N PHE A 84 SHEET 1 AA2 7 SER A 110 LYS A 111 0 SHEET 2 AA2 7 PHE A 137 ARG A 141 -1 O HIS A 140 N SER A 110 SHEET 3 AA2 7 ALA A 333 SER A 337 -1 O HIS A 336 N SER A 139 SHEET 4 AA2 7 GLN A 304 ALA A 310 1 N CYS A 305 O ALA A 333 SHEET 5 AA2 7 PHE A 156 ARG A 162 1 N TYR A 157 O LEU A 306 SHEET 6 AA2 7 LEU A 191 MET A 195 1 O GLN A 194 N ARG A 162 SHEET 7 AA2 7 THR A 232 SER A 236 1 O PHE A 235 N MET A 195 SHEET 1 AA3 2 PRO A 341 ALA A 342 0 SHEET 2 AA3 2 GLY A 345 LYS A 349 -1 O THR A 348 N ALA A 342 SHEET 1 AA4 2 PHE B 84 ASP B 86 0 SHEET 2 AA4 2 THR B 89 GLN B 91 -1 O GLN B 91 N PHE B 84 SHEET 1 AA5 7 SER B 110 LYS B 111 0 SHEET 2 AA5 7 PHE B 137 ARG B 141 -1 O HIS B 140 N SER B 110 SHEET 3 AA5 7 ALA B 333 SER B 337 -1 O HIS B 336 N SER B 139 SHEET 4 AA5 7 GLN B 304 ALA B 310 1 N CYS B 305 O ALA B 333 SHEET 5 AA5 7 PHE B 156 ARG B 162 1 N TYR B 157 O GLN B 304 SHEET 6 AA5 7 LEU B 191 MET B 195 1 O GLN B 194 N ARG B 162 SHEET 7 AA5 7 THR B 232 SER B 236 1 O PHE B 235 N MET B 195 SHEET 1 AA6 2 PRO B 341 ALA B 342 0 SHEET 2 AA6 2 GLY B 345 LYS B 349 -1 O THR B 348 N ALA B 342 LINK O GLY A 163 MG MG A 503 1555 1555 2.99 LINK OG SER A 165 MG MG A 503 1555 1555 2.87 LINK O1P TYM A 501 MG MG A 502 1555 1555 2.47 LINK MG MG A 502 O HOH A 635 1555 1555 2.55 LINK OD1 ASP B 312 MG MG B 502 1555 1555 2.43 LINK O2P TYM B 501 MG MG B 502 1555 1555 2.68 SITE 1 AC1 27 TYR A 159 THR A 160 GLY A 161 ARG A 162 SITE 2 AC1 27 GLY A 163 GLY A 172 HIS A 173 PRO A 176 SITE 3 AC1 27 GLN A 194 GLU A 199 GLN A 284 CYS A 309 SITE 4 AC1 27 ALA A 310 ASP A 312 GLN A 313 PHE A 317 SITE 5 AC1 27 THR A 338 PHE A 339 PHE A 340 LYS A 349 SITE 6 AC1 27 MET A 350 MG A 502 MG A 503 HOH A 601 SITE 7 AC1 27 HOH A 602 HOH A 610 HOH A 633 SITE 1 AC2 4 LYS A 200 TYM A 501 MG A 503 HOH A 635 SITE 1 AC3 6 ARG A 162 GLY A 163 SER A 165 TYM A 501 SITE 2 AC3 6 MG A 502 HOH A 602 SITE 1 AC4 23 TYR B 159 THR B 160 GLY B 161 ARG B 162 SITE 2 AC4 23 GLY B 163 GLY B 172 HIS B 173 PRO B 176 SITE 3 AC4 23 GLN B 194 GLU B 199 GLN B 284 CYS B 309 SITE 4 AC4 23 ALA B 310 ASP B 312 GLN B 313 PHE B 317 SITE 5 AC4 23 PHE B 339 PHE B 340 LYS B 349 MET B 350 SITE 6 AC4 23 MG B 502 HOH B 601 HOH B 605 SITE 1 AC5 3 ASP B 312 GLN B 313 TYM B 501 CRYST1 136.352 95.277 99.623 90.00 130.46 90.00 C 1 2 1 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 0.007334 0.000000 0.006254 0.00000 SCALE2 0.000000 0.010496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013192 0.00000