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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
