HEADER LIGASE 06-JUN-07 2Q7E TITLE THE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO AN ATP ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRROLYSYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: PYRROLYSINE--TRNA LIGASE, PYLRS; COMPND 6 EC: 6.1.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI; SOURCE 3 ORGANISM_TAXID: 2209; SOURCE 4 GENE: PYLS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 CODON PLUS-RIL(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS AMINOACYL-TRNA SYNTHETASE, PYRROLYSINE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KAVRAN,T.A.STEITZ REVDAT 4 21-FEB-24 2Q7E 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2Q7E 1 VERSN REVDAT 2 24-FEB-09 2Q7E 1 VERSN REVDAT 1 24-JUL-07 2Q7E 0 JRNL AUTH J.M.KAVRAN,S.GUNDLLAPALLI,P.O'DONOGHUE,M.ENGLERT,D.SOLL, JRNL AUTH 2 T.A.STEITZ JRNL TITL STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE, AN ARCHAEAL ENZYME JRNL TITL 2 FOR GENETIC CODE INNOVATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 11268 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17592110 JRNL DOI 10.1073/PNAS.0704769104 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 34.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 38485 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2042 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) : 2651 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2105 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 211 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52000 REMARK 3 B22 (A**2) : -0.52000 REMARK 3 B33 (A**2) : 0.77000 REMARK 3 B12 (A**2) : -0.26000 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): 0.089 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.852 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2267 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1666 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3042 ; 1.297 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4031 ; 0.842 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 6.218 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;33.606 ;23.578 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;12.782 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;13.330 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 324 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2439 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 463 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 394 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1744 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1056 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1231 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 161 ; 0.146 ; 0.200 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): 10 ; 0.144 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 61 ; 0.247 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.147 ; 0.200 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): 1730 ; 4.138 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 532 ; 1.024 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2130 ; 4.654 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1107 ; 4.630 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 908 ; 6.182 ; 3.000 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 188 A 454 REMARK 3 ORIGIN FOR THE GROUP (A): 16.8093 38.4761 29.1258 REMARK 3 T TENSOR REMARK 3 T11: -0.1811 T22: -0.1196 REMARK 3 T33: -0.1593 T12: 0.0086 REMARK 3 T13: -0.0123 T23: 0.0226 REMARK 3 L TENSOR REMARK 3 L11: 1.3730 L22: 2.2891 REMARK 3 L33: 0.8678 L12: -0.6703 REMARK 3 L13: 0.4382 L23: -0.2000 REMARK 3 S TENSOR REMARK 3 S11: 0.0107 S12: -0.1204 S13: -0.1842 REMARK 3 S21: 0.0789 S22: 0.0557 S23: 0.2779 REMARK 3 S31: 0.1142 S32: -0.1857 S33: -0.0664 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 REMARK 4 REMARK 4 2Q7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043242. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97917 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : SI 111 REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38485 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.2000 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.87900 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: SIRAS REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS 10% PEG2000 MME , PH 7.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,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 23.43800 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 46.87600 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.43800 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 46.87600 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 11090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.0 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 -1.000000 0.000000 0.000000 52.56200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 91.04005 REMARK 350 BIOMT3 2 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 164 REMARK 465 GLY A 165 REMARK 465 SER A 166 REMARK 465 SER A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 SER A 174 REMARK 465 SER A 175 REMARK 465 GLY A 176 REMARK 465 LEU A 177 REMARK 465 VAL A 178 REMARK 465 PRO A 179 REMARK 465 ARG A 180 REMARK 465 GLY A 181 REMARK 465 SER A 182 REMARK 465 HIS A 183 REMARK 465 MET A 184 REMARK 465 ALA A 185 REMARK 465 SER A 186 REMARK 465 ALA A 187 REMARK 465 ILE A 208 REMARK 465 SER A 209 REMARK 465 LEU A 210 REMARK 465 ASN A 211 REMARK 465 SER A 212 REMARK 465 GLY A 213 REMARK 465 ASP A 281 REMARK 465 THR A 282 REMARK 465 GLU A 283 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 GLU A 237 -87.99 -107.29 REMARK 500 ASP A 292 -162.61 56.74 REMARK 500 TYR A 384 -73.80 -104.89 REMARK 500 ASP A 386 78.70 60.62 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 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 396 OE2 REMARK 620 2 GLU A 396 OE1 49.6 REMARK 620 3 SER A 399 OG 82.2 90.8 REMARK 620 4 ANP A 900 O1B 89.7 95.8 162.4 REMARK 620 5 ANP A 900 O2A 80.9 130.4 84.3 79.0 REMARK 620 6 HOH A1117 O 116.4 68.5 85.6 112.0 158.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP A 900 O2G REMARK 620 2 ANP A 900 O2B 89.2 REMARK 620 3 HOH A1002 O 95.8 93.0 REMARK 620 4 HOH A1004 O 172.0 85.7 90.6 REMARK 620 5 HOH A1006 O 88.4 95.4 170.6 86.0 REMARK 620 6 HOH A1014 O 92.8 175.7 83.0 92.7 88.4 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 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 ANP A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 911 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q7H RELATED DB: PDB REMARK 900 THE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO ADENYLATED REMARK 900 PYRROLYSINE AND PYROPHOSPHATE REMARK 900 RELATED ID: 2Q7G RELATED DB: PDB REMARK 900 THE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO A PYRROLYSINE REMARK 900 ANALGOUE (CYC) AND ATP DBREF 2Q7E A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 2Q7E MET A 164 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E GLY A 165 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E SER A 166 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E SER A 167 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E HIS A 168 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7E HIS A 169 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7E HIS A 170 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7E HIS A 171 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7E HIS A 172 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7E HIS A 173 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7E SER A 174 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E SER A 175 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E GLY A 176 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E LEU A 177 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E VAL A 178 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E PRO A 179 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E ARG A 180 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E GLY A 181 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E SER A 182 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E HIS A 183 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7E MET A 184 UNP Q8PWY1 CLONING ARTIFACT SEQRES 1 A 291 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 291 LEU VAL PRO ARG GLY SER HIS MET ALA SER ALA PRO ALA SEQRES 3 A 291 LEU THR LYS SER GLN THR ASP ARG LEU GLU VAL LEU LEU SEQRES 4 A 291 ASN PRO LYS ASP GLU ILE SER LEU ASN SER GLY LYS PRO SEQRES 5 A 291 PHE ARG GLU LEU GLU SER GLU LEU LEU SER ARG ARG LYS SEQRES 6 A 291 LYS ASP LEU GLN GLN ILE TYR ALA GLU GLU ARG GLU ASN SEQRES 7 A 291 TYR LEU GLY LYS LEU GLU ARG GLU ILE THR ARG PHE PHE SEQRES 8 A 291 VAL ASP ARG GLY PHE LEU GLU ILE LYS SER PRO ILE LEU SEQRES 9 A 291 ILE PRO LEU GLU TYR ILE GLU ARG MET GLY ILE ASP ASN SEQRES 10 A 291 ASP THR GLU LEU SER LYS GLN ILE PHE ARG VAL ASP LYS SEQRES 11 A 291 ASN PHE CYS LEU ARG PRO MET LEU ALA PRO ASN LEU TYR SEQRES 12 A 291 ASN TYR LEU ARG LYS LEU ASP ARG ALA LEU PRO ASP PRO SEQRES 13 A 291 ILE LYS ILE PHE GLU ILE GLY PRO CYS TYR ARG LYS GLU SEQRES 14 A 291 SER ASP GLY LYS GLU HIS LEU GLU GLU PHE THR MET LEU SEQRES 15 A 291 ASN PHE CYS GLN MET GLY SER GLY CYS THR ARG GLU ASN SEQRES 16 A 291 LEU GLU SER ILE ILE THR ASP PHE LEU ASN HIS LEU GLY SEQRES 17 A 291 ILE ASP PHE LYS ILE VAL GLY ASP SER CYS MET VAL TYR SEQRES 18 A 291 GLY ASP THR LEU ASP VAL MET HIS GLY ASP LEU GLU LEU SEQRES 19 A 291 SER SER ALA VAL VAL GLY PRO ILE PRO LEU ASP ARG GLU SEQRES 20 A 291 TRP GLY ILE ASP LYS PRO TRP ILE GLY ALA GLY PHE GLY SEQRES 21 A 291 LEU GLU ARG LEU LEU LYS VAL LYS HIS ASP PHE LYS ASN SEQRES 22 A 291 ILE LYS ARG ALA ALA ARG SER GLU SER TYR TYR ASN GLY SEQRES 23 A 291 ILE SER THR ASN LEU HET MG A 501 1 HET MG A 502 1 HET ANP A 900 31 HET EDO A 901 4 HET EDO A 902 4 HET EDO A 903 4 HET EDO A 904 4 HET EDO A 905 4 HET EDO A 906 4 HET EDO A 907 4 HET EDO A 908 4 HET EDO A 909 4 HET EDO A 910 4 HET EDO A 911 4 HETNAM MG MAGNESIUM ION HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG 2(MG 2+) FORMUL 4 ANP C10 H17 N6 O12 P3 FORMUL 5 EDO 11(C2 H6 O2) FORMUL 16 HOH *211(H2 O) HELIX 1 1 THR A 191 LEU A 202 1 12 HELIX 2 2 PRO A 215 GLU A 237 1 23 HELIX 3 3 ASN A 241 ARG A 257 1 17 HELIX 4 4 LEU A 270 MET A 276 1 7 HELIX 5 5 LEU A 284 ILE A 288 5 5 HELIX 6 6 LEU A 301 ASP A 313 1 13 HELIX 7 7 THR A 355 GLY A 371 1 17 HELIX 8 8 ILE A 405 GLY A 412 5 8 HELIX 9 9 LEU A 424 ASP A 433 1 10 HELIX 10 10 ASN A 436 ALA A 441 5 6 SHEET 1 A 7 LEU A 260 ILE A 262 0 SHEET 2 A 7 ILE A 320 TYR A 329 1 O LYS A 321 N LEU A 260 SHEET 3 A 7 GLU A 341 MET A 350 -1 O MET A 344 N GLY A 326 SHEET 4 A 7 TRP A 417 GLY A 423 -1 O PHE A 422 N LEU A 345 SHEET 5 A 7 LEU A 395 VAL A 402 -1 N VAL A 401 O GLY A 419 SHEET 6 A 7 ASP A 386 HIS A 392 -1 N LEU A 388 O ALA A 400 SHEET 7 A 7 LYS A 375 SER A 380 -1 N VAL A 377 O ASP A 389 SHEET 1 B 3 LEU A 267 PRO A 269 0 SHEET 2 B 3 PHE A 295 LEU A 297 -1 O CYS A 296 N ILE A 268 SHEET 3 B 3 ARG A 290 VAL A 291 -1 N VAL A 291 O PHE A 295 SHEET 1 C 2 TYR A 446 TYR A 447 0 SHEET 2 C 2 ILE A 450 SER A 451 -1 O ILE A 450 N TYR A 447 LINK OE2 GLU A 396 MG MG A 502 1555 1555 2.48 LINK OE1 GLU A 396 MG MG A 502 1555 1555 2.70 LINK OG SER A 399 MG MG A 502 1555 1555 2.32 LINK MG MG A 501 O2G ANP A 900 1555 1555 2.11 LINK MG MG A 501 O2B ANP A 900 1555 1555 2.11 LINK MG MG A 501 O HOH A1002 1555 1555 2.18 LINK MG MG A 501 O HOH A1004 1555 1555 2.16 LINK MG MG A 501 O HOH A1006 1555 1555 2.15 LINK MG MG A 501 O HOH A1014 1555 1555 2.09 LINK MG MG A 502 O1B ANP A 900 1555 1555 2.19 LINK MG MG A 502 O2A ANP A 900 1555 1555 2.50 LINK MG MG A 502 O HOH A1117 1555 1555 2.25 CISPEP 1 LYS A 214 PRO A 215 0 -16.86 CISPEP 2 ASP A 318 PRO A 319 0 -4.23 CISPEP 3 GLY A 385 ASP A 386 0 1.97 CISPEP 4 GLY A 403 PRO A 404 0 1.18 SITE 1 AC1 5 ANP A 900 HOH A1002 HOH A1004 HOH A1006 SITE 2 AC1 5 HOH A1014 SITE 1 AC2 4 GLU A 396 SER A 399 ANP A 900 HOH A1117 SITE 1 AC3 25 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC3 25 PHE A 342 MET A 344 GLU A 396 LEU A 397 SITE 3 AC3 25 SER A 398 SER A 399 GLY A 421 GLY A 423 SITE 4 AC3 25 ARG A 426 MG A 501 MG A 502 EDO A 906 SITE 5 AC3 25 HOH A 912 HOH A1002 HOH A1004 HOH A1006 SITE 6 AC3 25 HOH A1014 HOH A1088 HOH A1106 HOH A1115 SITE 7 AC3 25 HOH A1118 SITE 1 AC4 6 ASN A 241 ARG A 439 ALA A 440 ASN A 448 SITE 2 AC4 6 GLY A 449 HOH A 963 SITE 1 AC5 7 TYR A 242 LYS A 245 LEU A 246 GLU A 249 SITE 2 AC5 7 LYS A 431 HIS A 432 HOH A1090 SITE 1 AC6 4 ASP A 256 ARG A 257 HIS A 369 HOH A 937 SITE 1 AC7 6 ASP A 373 LYS A 375 MET A 391 HIS A 392 SITE 2 AC7 6 GLY A 393 EDO A 909 SITE 1 AC8 7 ASP A 313 MET A 350 GLY A 412 ILE A 413 SITE 2 AC8 7 ASP A 414 LYS A 415 HOH A 994 SITE 1 AC9 6 HIS A 338 ASP A 394 GLU A 396 ARG A 426 SITE 2 AC9 6 ANP A 900 HOH A1088 SITE 1 BC1 5 ALA A 302 TYR A 306 TYR A 384 TRP A 417 SITE 2 BC1 5 HOH A1023 SITE 1 BC2 4 ARG A 257 ASP A 365 HOH A 938 HOH A1105 SITE 1 BC3 4 ASP A 373 HIS A 392 GLY A 393 EDO A 904 SITE 1 BC4 7 TYR A 272 ASN A 307 ARG A 310 LYS A 311 SITE 2 BC4 7 GLU A 357 GLU A 444 HOH A 987 SITE 1 BC5 2 GLU A 237 HOH A1098 CRYST1 105.124 105.124 70.314 90.00 90.00 120.00 P 64 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 0.009513 0.005492 0.000000 0.00000 SCALE2 0.000000 0.010984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014222 0.00000