HEADER LIGASE 06-JUN-07 2Q7G TITLE PYRROLYSINE TRNA SYNTHETASE BOUND TO A PYRROLYSINE ANALOGUE (CYC) AND TITLE 2 ATP 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 PYRROLYSYL-TRNA SYNTETHETASE, PYRROLYSINE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KAVRAN,T.A.STEITZ REVDAT 4 21-FEB-24 2Q7G 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2Q7G 1 VERSN REVDAT 2 24-FEB-09 2Q7G 1 VERSN REVDAT 1 24-JUL-07 2Q7G 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 33104 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1730 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2071 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2046 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 251 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) : 35.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 0.82000 REMARK 3 B12 (A**2) : -0.27000 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): 0.101 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.870 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2224 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1637 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2978 ; 1.282 ; 2.024 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3939 ; 0.812 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ; 6.047 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;32.199 ;23.679 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 415 ;12.537 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;13.094 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 319 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2365 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 446 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 437 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1771 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1028 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1203 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 187 ; 0.162 ; 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 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 69 ; 0.242 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.148 ; 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): 1692 ; 3.946 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 516 ; 0.920 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2073 ; 4.354 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1088 ; 4.453 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 899 ; 5.814 ; 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): 17.1930 38.2359 29.3146 REMARK 3 T TENSOR REMARK 3 T11: -0.2039 T22: -0.1496 REMARK 3 T33: -0.1682 T12: 0.0052 REMARK 3 T13: -0.0123 T23: 0.0278 REMARK 3 L TENSOR REMARK 3 L11: 1.6249 L22: 2.3933 REMARK 3 L33: 0.9032 L12: -0.8636 REMARK 3 L13: 0.4062 L23: -0.2209 REMARK 3 S TENSOR REMARK 3 S11: 0.0163 S12: -0.1306 S13: -0.2297 REMARK 3 S21: 0.0901 S22: 0.0684 S23: 0.2773 REMARK 3 S31: 0.1392 S32: -0.1648 S33: -0.0848 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 2Q7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-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 : NSLS REMARK 200 BEAMLINE : X29A 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 : NULL 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 : 33104 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM 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 23.86467 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 47.72933 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 23.86467 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 47.72933 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: 10520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 52.38650 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 90.73608 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 ASN A 280 REMARK 465 ASP A 281 REMARK 465 THR A 282 REMARK 465 GLU A 283 REMARK 465 ASP A 379 REMARK 465 SER A 380 REMARK 465 CYS A 381 REMARK 465 MET A 382 REMARK 465 VAL A 383 REMARK 465 TYR A 384 REMARK 465 GLY A 385 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 257 NE - CZ - NH1 ANGL. DEV. = 3.1 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 GLU A 237 -89.83 -109.02 REMARK 500 ASP A 292 -153.24 53.31 REMARK 500 ASP A 414 38.78 -140.74 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 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 396 OE2 REMARK 620 2 SER A 399 OG 83.3 REMARK 620 3 ATP A 900 O1B 95.1 177.0 REMARK 620 4 ATP A 900 O2A 95.6 90.5 92.2 REMARK 620 5 HOH A1125 O 101.1 89.9 87.9 163.2 REMARK 620 6 HOH A1158 O 167.5 84.2 97.3 84.8 78.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 900 O2G REMARK 620 2 ATP A 900 O2B 91.1 REMARK 620 3 HOH A 996 O 94.9 99.4 REMARK 620 4 HOH A 998 O 177.0 90.1 87.7 REMARK 620 5 HOH A1087 O 87.8 95.9 164.3 89.3 REMARK 620 6 HOH A1088 O 91.3 177.3 81.7 87.5 82.9 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 908 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 909 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 910 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 911 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CCL A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q7E RELATED DB: PDB REMARK 900 THE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO AN ATP ANALOGUE REMARK 900 RELATED ID: 2Q7H RELATED DB: PDB REMARK 900 THE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO ADENYLATED REMARK 900 PYRROLYSINE AND PYROPHOSPHATE DBREF 2Q7G A 185 454 UNP Q8PWY1 PYLS_METMA 185 454 SEQADV 2Q7G MET A 164 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G GLY A 165 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G SER A 166 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G SER A 167 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G HIS A 168 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7G HIS A 169 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7G HIS A 170 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7G HIS A 171 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7G HIS A 172 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7G HIS A 173 UNP Q8PWY1 EXPRESSION TAG SEQADV 2Q7G SER A 174 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G SER A 175 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G GLY A 176 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G LEU A 177 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G VAL A 178 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G PRO A 179 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G ARG A 180 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G GLY A 181 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G SER A 182 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G HIS A 183 UNP Q8PWY1 CLONING ARTIFACT SEQADV 2Q7G 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 500 1 HET MG A 501 1 HET ATP A 900 31 HET EDO A 902 4 HET EDO A 903 4 HET EDO A 907 4 HET EDO A 908 4 HET EDO A 904 4 HET EDO A 909 4 HET EDO A 910 4 HET EDO A 905 4 HET EDO A 911 4 HET EDO A 906 4 HET CCL A 901 18 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM CCL N~6~-[(CYCLOPENTYLOXY)CARBONYL]-D-LYSINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG 2(MG 2+) FORMUL 4 ATP C10 H16 N5 O13 P3 FORMUL 5 EDO 10(C2 H6 O2) FORMUL 15 CCL C12 H22 N2 O4 FORMUL 16 HOH *251(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 350 N ILE A 320 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 THR A 387 HIS A 392 -1 N HIS A 392 O LEU A 395 SHEET 7 A 7 LYS A 375 VAL A 377 -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 501 1555 1555 2.41 LINK OG SER A 399 MG MG A 501 1555 1555 2.24 LINK MG MG A 500 O2G ATP A 900 1555 1555 2.04 LINK MG MG A 500 O2B ATP A 900 1555 1555 2.02 LINK MG MG A 500 O HOH A 996 1555 1555 2.18 LINK MG MG A 500 O HOH A 998 1555 1555 2.18 LINK MG MG A 500 O HOH A1087 1555 1555 2.18 LINK MG MG A 500 O HOH A1088 1555 1555 2.17 LINK MG MG A 501 O1B ATP A 900 1555 1555 2.00 LINK MG MG A 501 O2A ATP A 900 1555 1555 2.31 LINK MG MG A 501 O HOH A1125 1555 1555 2.19 LINK MG MG A 501 O HOH A1158 1555 1555 2.19 CISPEP 1 LYS A 214 PRO A 215 0 -18.71 CISPEP 2 ASP A 318 PRO A 319 0 -1.27 CISPEP 3 GLY A 403 PRO A 404 0 -0.64 SITE 1 AC1 5 ATP A 900 HOH A 996 HOH A 998 HOH A1087 SITE 2 AC1 5 HOH A1088 SITE 1 AC2 5 GLU A 396 SER A 399 ATP A 900 HOH A1125 SITE 2 AC2 5 HOH A1158 SITE 1 AC3 27 ARG A 330 GLU A 332 HIS A 338 LEU A 339 SITE 2 AC3 27 PHE A 342 MET A 344 GLU A 396 LEU A 397 SITE 3 AC3 27 SER A 398 SER A 399 GLY A 421 GLY A 423 SITE 4 AC3 27 ARG A 426 MG A 500 MG A 501 CCL A 901 SITE 5 AC3 27 EDO A 906 HOH A 912 HOH A 996 HOH A 998 SITE 6 AC3 27 HOH A1087 HOH A1088 HOH A1125 HOH A1126 SITE 7 AC3 27 HOH A1128 HOH A1158 HOH A1160 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 960 SITE 1 AC5 5 TYR A 242 LEU A 246 GLU A 249 LYS A 431 SITE 2 AC5 5 HIS A 432 SITE 1 AC6 4 ASP A 373 HIS A 392 GLY A 393 EDO A 904 SITE 1 AC7 7 TYR A 272 ASN A 307 ARG A 310 LYS A 311 SITE 2 AC7 7 GLU A 357 GLU A 444 HOH A 983 SITE 1 AC8 6 ASP A 373 LYS A 375 MET A 391 HIS A 392 SITE 2 AC8 6 GLY A 393 EDO A 907 SITE 1 AC9 4 SER A 225 EDO A 910 HOH A 975 HOH A 980 SITE 1 BC1 3 SER A 221 LYS A 228 EDO A 909 SITE 1 BC2 6 ARG A 310 ASP A 313 GLY A 412 ILE A 413 SITE 2 BC2 6 ASP A 414 LYS A 415 SITE 1 BC3 5 LEU A 339 GLU A 340 GLU A 341 ALA A 441 SITE 2 BC3 5 HOH A 988 SITE 1 BC4 5 GLU A 337 HIS A 338 ASP A 394 GLU A 396 SITE 2 BC4 5 ATP A 900 SITE 1 BC5 12 ALA A 302 LEU A 305 TYR A 306 ASN A 346 SITE 2 BC5 12 SER A 399 TRP A 417 GLY A 419 ALA A 420 SITE 3 BC5 12 GLY A 421 ATP A 900 HOH A1155 HOH A1157 CRYST1 104.773 104.773 71.594 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 0.009544 0.005510 0.000000 0.00000 SCALE2 0.000000 0.011021 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013968 0.00000