HEADER LIGASE 19-FEB-08 2ZIM
TITLE PYRROLYSYL-TRNA SYNTHETASE BOUND TO ADENYLATED PYRROLYSINE AND
TITLE 2 PYROPHOSPHATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PYRROLYSYL-TRNA SYNTHETASE;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, UNP RESIDUES 185-454;
COMPND 5 SYNONYM: PYRROLYSINE--TRNA LIGASE, PYLRS;
COMPND 6 EC: 6.1.1.26;
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 CODONPLUS RIL (DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS TRNA SYNTHETASE BOUND TO AN ADENYLATED INTERMEDIATE, AMINOACYL-TRNA
KEYWDS 2 SYNTHETASE, ATP-BINDING, LIGASE, NUCLEOTIDE-BINDING, PROTEIN
KEYWDS 3 BIOSYNTHESIS
EXPDTA X-RAY DIFFRACTION
AUTHOR T.A.STEITZ,J.M.KAVRAN
REVDAT 5 21-FEB-24 2ZIM 1 REMARK SEQADV
REVDAT 4 11-OCT-17 2ZIM 1 REMARK
REVDAT 3 10-AUG-11 2ZIM 1 REMARK
REVDAT 2 24-FEB-09 2ZIM 1 VERSN
REVDAT 1 04-MAR-08 2ZIM 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. 2.10 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) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.40
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 24560
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) : 0.188
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.228
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1311
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) : 1794
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89
REMARK 3 BIN R VALUE (WORKING SET) : 0.2820
REMARK 3 BIN FREE R VALUE SET COUNT : 105
REMARK 3 BIN FREE R VALUE : 0.3210
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2116
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 89
REMARK 3 SOLVENT ATOMS : 186
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.03
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.42000
REMARK 3 B22 (A**2) : -0.42000
REMARK 3 B33 (A**2) : 0.63000
REMARK 3 B12 (A**2) : -0.21000
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): 0.161
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.283
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2274 ; 0.020 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3049 ; 1.835 ; 2.025
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 267 ; 7.036 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;33.348 ;23.645
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 422 ;15.530 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;20.025 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 326 ; 0.135 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1670 ; 0.008 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 990 ; 0.215 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1462 ; 0.308 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 179 ; 0.178 ; 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): 60 ; 0.183 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.230 ; 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): 1373 ; 1.339 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2140 ; 2.173 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1019 ; 3.095 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 906 ; 4.819 ; 4.500
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 : 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 2ZIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-08.
REMARK 100 THE DEPOSITION ID IS D_1000028018.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-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) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : OTHER
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.514
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25910
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
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 (%) : NULL
REMARK 200 DATA REDUNDANCY : 11.20
REMARK 200 R MERGE (I) : 0.08700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.1000
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) : 2.18
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
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 (%): 63.29
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, 10% PEG2000-MME, PH 7.5,
REMARK 280 VAPOR DIFFUSION, TEMPERATURE 289 K
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 23.42067
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 46.84133
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 23.42067
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 46.84133
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: 11370 ANGSTROM**2
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 52.53500
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 90.99329
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 ASN A 280
REMARK 465 ASP A 281
REMARK 465 THR A 282
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH A 932 O HOH A 1059 2.13
REMARK 500 NE2 HIS A 338 O1 POP A 901 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 939 O HOH A 1044 4665 2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU A 271 CG GLU A 271 CD 0.096
REMARK 500
REMARK 500 REMARK: NULL
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 298 NE - CZ - NH2 ANGL. DEV. = -3.0 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 -86.65 -104.55
REMARK 500 ASP A 292 -168.22 57.82
REMARK 500 ASP A 386 74.98 74.79
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 902
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 903
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 904
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 905
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 906
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 909
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 910
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 911
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YLY A 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 901
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2Q7G RELATED DB: PDB
REMARK 900 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO A PYRROLYSINE
REMARK 900 ANALGOUE (CYC) AND ATP
REMARK 900 RELATED ID: 2Q7E RELATED DB: PDB
REMARK 900 STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO AN ATP ANALOGUE
REMARK 900 RELATED ID: 2Q7H RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO ADENYLATED
REMARK 900 PYRROLYSINE AND PYROPHOSPHATE, PREVIOUS REFINEMENT
DBREF 2ZIM A 185 454 UNP Q8PWY1 PYLS_METMA 185 454
SEQADV 2ZIM MET A 164 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM GLY A 165 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM SER A 166 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM SER A 167 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM HIS A 168 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM HIS A 169 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM HIS A 170 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM HIS A 171 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM HIS A 172 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM HIS A 173 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM SER A 174 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM SER A 175 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM GLY A 176 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM LEU A 177 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM VAL A 178 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM PRO A 179 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM ARG A 180 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM GLY A 181 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM SER A 182 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM HIS A 183 UNP Q8PWY1 EXPRESSION TAG
SEQADV 2ZIM MET A 184 UNP Q8PWY1 EXPRESSION TAG
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 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
HET YLY A 1 40
HET POP A 901 9
HETNAM EDO 1,2-ETHANEDIOL
HETNAM YLY (2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-
HETNAM 2 YLY YL]CARBONYL}AMINO)HEXANOYL [(2S,3R,4R,5R)-5-(6-AMINO-
HETNAM 3 YLY 9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-
HETNAM 4 YLY YL]METHYL HYDROGEN (R)-PHOSPHATE
HETNAM POP PYROPHOSPHATE 2-
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 EDO 10(C2 H6 O2)
FORMUL 12 YLY C22 H35 N8 O9 P
FORMUL 13 POP H2 O7 P2 2-
FORMUL 14 HOH *186(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 PHE A 342 N CYS A 328
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 SER A 399 O GLY A 421
SHEET 6 A 7 GLY A 385 HIS A 392 -1 N LEU A 388 O ALA A 400
SHEET 7 A 7 LYS A 375 CYS A 381 -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
CISPEP 1 SER A 212 GLY A 213 0 -10.63
CISPEP 2 ASP A 318 PRO A 319 0 -3.30
CISPEP 3 GLY A 385 ASP A 386 0 8.30
CISPEP 4 GLY A 403 PRO A 404 0 3.58
SITE 1 AC1 7 ASN A 241 ARG A 439 ALA A 440 ALA A 441
SITE 2 AC1 7 ASN A 448 GLY A 449 HOH A 961
SITE 1 AC2 7 TYR A 242 LYS A 245 LEU A 246 GLU A 249
SITE 2 AC2 7 LEU A 428 LYS A 431 HIS A 432
SITE 1 AC3 6 PHE A 253 ASP A 256 ARG A 257 HIS A 369
SITE 2 AC3 6 HOH A 936 HOH A1061
SITE 1 AC4 6 ASP A 373 PHE A 374 LYS A 375 HIS A 392
SITE 2 AC4 6 GLY A 393 HOH A1093
SITE 1 AC5 7 ASP A 313 MET A 350 GLY A 412 ILE A 413
SITE 2 AC5 7 ASP A 414 LYS A 415 HOH A 991
SITE 1 AC6 6 GLU A 337 HIS A 338 ASP A 394 LEU A 395
SITE 2 AC6 6 GLU A 396 ARG A 426
SITE 1 AC7 5 ARG A 257 ILE A 362 ASP A 365 HOH A 937
SITE 2 AC7 5 HOH A1080
SITE 1 AC8 2 ASP A 373 HIS A 392
SITE 1 AC9 6 TYR A 272 ASN A 307 ARG A 310 LYS A 311
SITE 2 AC9 6 GLU A 357 HOH A 984
SITE 1 BC1 4 GLN A 233 ALA A 236 GLU A 237 HOH A1075
SITE 1 BC2 23 MET A 300 ALA A 302 LEU A 305 TYR A 306
SITE 2 BC2 23 ARG A 330 GLU A 332 LEU A 339 PHE A 342
SITE 3 BC2 23 MET A 344 ASN A 346 TYR A 384 GLU A 396
SITE 4 BC2 23 LEU A 397 SER A 398 SER A 399 TRP A 417
SITE 5 BC2 23 GLY A 419 GLY A 421 GLY A 423 ARG A 426
SITE 6 BC2 23 HOH A 912 HOH A1086 HOH A1094
SITE 1 BC3 5 ARG A 330 HIS A 338 GLU A 396 ARG A 426
SITE 2 BC3 5 HOH A1094
CRYST1 105.070 105.070 70.262 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 0.009517 0.005495 0.000000 0.00000
SCALE2 0.000000 0.010990 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014232 0.00000