HEADER LIGASE/RNA 13-NOV-02 1N78 TITLE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLUTAMYL-TRNA SYNTHETASE TITLE 2 COMPLEXED WITH TRNA(GLU) AND GLUTAMOL-AMP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA(GLU); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GLUTAMYL-TRNA SYNTHETASE; COMPND 7 CHAIN: A, B; COMPND 8 SYNONYM: GLURS, GLUTAMATE--TRNA LIGASE; COMPND 9 EC: 6.1.1.17; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS T-RNA OCCURS FROM THERMUS THERMOPHILUS, IN VITRO SOURCE 4 TRANSCRIPTION; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 7 ORGANISM_TAXID: 274; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PK7 KEYWDS ERS/TRNA/GOA, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 2 STRUCTURAL GENOMICS, LIGASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.SEKINE,O.NUREKI,D.Y.DUBOIS,S.BERNIER,R.CHENEVERT,J.LAPOINTE, AUTHOR 2 D.G.VASSYLYEV,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 3 INITIATIVE (RSGI) REVDAT 3 25-OCT-23 1N78 1 REMARK LINK REVDAT 2 24-FEB-09 1N78 1 VERSN REVDAT 1 25-FEB-03 1N78 0 JRNL AUTH S.SEKINE,O.NUREKI,D.Y.DUBOIS,S.BERNIER,R.CHENEVERT, JRNL AUTH 2 J.LAPOINTE,D.G.VASSYLYEV,S.YOKOYAMA JRNL TITL ATP BINDING BY GLUTAMYL-TRNA SYNTHETASE IS SWITCHED TO THE JRNL TITL 2 PRODUCTIVE MODE BY TRNA BINDING JRNL REF EMBO J. V. 22 676 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12554668 JRNL DOI 10.1093/EMBOJ/CDG053 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.SEKINE,O.NUREKI,A.SHIMADA,D.G.VASSYLYEV,S.YOKOYAMA REMARK 1 TITL STRUCTURAL BASIS FOR ANTICODON RECOGNITION BY DISCRIMINATING REMARK 1 TITL 2 GLUTAMYL-TRNA SYNTHETASE REMARK 1 REF NAT.STRUCT.BIOL. V. 8 203 2001 REMARK 1 REFN ISSN 1072-8368 REMARK 1 DOI 10.1038/84927 REMARK 1 REFERENCE 2 REMARK 1 AUTH O.NUREKI,D.G.VASSYLYEV,K.KATAYANAGI,T.SHIMIZU,S.SEKINE, REMARK 1 AUTH 2 T.KIGAWA,T.MIYAZAWA,S.YOKOYAMA,K.MORIKAWA REMARK 1 TITL ARCHITECTURES OF CLASS-DEFINING AND SPECIFIC DOMAINS OF REMARK 1 TITL 2 GLUTAMYL-TRNA SYNTHETASE REMARK 1 REF SCIENCE V. 267 1958 1995 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 5656722.200 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 90631 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 SET) : 0.219 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4574 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 9552 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 518 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7628 REMARK 3 NUCLEIC ACID ATOMS : 3194 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 751 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.23000 REMARK 3 B22 (A**2) : -4.03000 REMARK 3 B33 (A**2) : 1.80000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.41 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.42 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.410 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.270 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.840 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.780 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 52.61 REMARK 3 REMARK 3 NCS MODEL : CONSTR REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 4 : GLA1.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 4 : GLA1.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1N78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017605. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92817 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: PDB 1G59 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1500, PH 6.7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.55950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.55950 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 1.000000 0.000000 0.000000 55.24600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 109.93500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.24600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 109.93500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.55950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.24600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 109.93500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.55950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.24600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 109.93500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: C, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 G C 501 P G C 501 OP3 -0.085 REMARK 500 G D 501 P G D 501 OP3 -0.084 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 G C 518 C2' - C3' - O3' ANGL. DEV. = 11.8 DEGREES REMARK 500 G C 519 C2' - C3' - O3' ANGL. DEV. = 11.2 DEGREES REMARK 500 A C 573 C2' - C3' - O3' ANGL. DEV. = 11.3 DEGREES REMARK 500 C C 574 C2' - C3' - O3' ANGL. DEV. = 12.6 DEGREES REMARK 500 A D 507 C2' - C3' - O3' ANGL. DEV. = 13.5 DEGREES REMARK 500 G D 518 C2' - C3' - O3' ANGL. DEV. = 12.4 DEGREES REMARK 500 G D 519 C2' - C3' - O3' ANGL. DEV. = 11.2 DEGREES REMARK 500 A D 573 C2' - C3' - O3' ANGL. DEV. = 10.4 DEGREES REMARK 500 C D 574 C2' - C3' - O3' ANGL. DEV. = 10.9 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 ASP A 42 68.86 -101.64 REMARK 500 ILE A 244 137.05 -37.29 REMARK 500 ASP B 42 45.32 -107.08 REMARK 500 SER B 181 -9.71 -58.61 REMARK 500 LYS B 241 -4.29 77.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G C 515 0.05 SIDE CHAIN REMARK 500 A D 545 0.06 SIDE CHAIN 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 C 700 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C2317 O REMARK 620 2 HOH C2318 O 158.4 REMARK 620 3 HOH C2319 O 81.3 77.2 REMARK 620 4 HOH C2320 O 90.0 111.2 170.1 REMARK 620 5 HOH C2321 O 87.7 100.6 105.8 78.3 REMARK 620 6 HOH C2322 O 85.6 91.1 88.1 86.6 163.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 701 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D2323 O REMARK 620 2 HOH D2324 O 159.0 REMARK 620 3 HOH D2325 O 79.7 103.8 REMARK 620 4 HOH D2326 O 79.7 89.6 152.8 REMARK 620 5 HOH D2327 O 77.4 83.9 72.9 85.4 REMARK 620 6 HOH D2328 O 92.9 107.9 85.6 113.0 157.6 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 C 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOM A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOM B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G59 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLURS/TRNA(GLU) BINARY REMARK 900 COMPLEX. REMARK 900 RELATED ID: 1GLN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLURS. REMARK 900 RELATED ID: 1J09 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLURS COMPLEXED WITH ATP REMARK 900 AND GLU. REMARK 900 RELATED ID: 1N75 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLURS COMPLEXED WITH ATP. REMARK 900 RELATED ID: 1N77 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS GLURS COMPLEXED WITH REMARK 900 TRNA(GLU) AND ATP. REMARK 900 RELATED ID: TTK003000897.5 RELATED DB: TARGETDB DBREF 1N78 A 1 468 UNP P27000 SYE_THET8 1 468 DBREF 1N78 B 1 468 UNP P27000 SYE_THET8 1 468 DBREF 1N78 C 501 576 PDB 1N78 1N78 501 576 DBREF 1N78 D 501 576 PDB 1N78 1N78 501 576 SEQADV 1N78 GLY A 74 UNP P27000 ALA 74 SEE REMARK 999 SEQADV 1N78 GLY A 75 UNP P27000 ALA 75 SEE REMARK 999 SEQADV 1N78 HIS A 77 UNP P27000 THR 77 SEE REMARK 999 SEQADV 1N78 GLY B 74 UNP P27000 ALA 74 SEE REMARK 999 SEQADV 1N78 GLY B 75 UNP P27000 ALA 75 SEE REMARK 999 SEQADV 1N78 HIS B 77 UNP P27000 THR 77 SEE REMARK 999 SEQRES 1 C 75 G G C C C C A U C G U C U SEQRES 2 C 75 A G C G G U U A G G A C G SEQRES 3 C 75 C G G C C C U C U C A A G SEQRES 4 C 75 G C C G A A A C G G G G G SEQRES 5 C 75 U U C G A U U C C C C C U SEQRES 6 C 75 G G G G U C A C C A SEQRES 1 D 75 G G C C C C A U C G U C U SEQRES 2 D 75 A G C G G U U A G G A C G SEQRES 3 D 75 C G G C C C U C U C A A G SEQRES 4 D 75 G C C G A A A C G G G G G SEQRES 5 D 75 U U C G A U U C C C C C U SEQRES 6 D 75 G G G G U C A C C A SEQRES 1 A 468 MET VAL VAL THR ARG ILE ALA PRO SER PRO THR GLY ASP SEQRES 2 A 468 PRO HIS VAL GLY THR ALA TYR ILE ALA LEU PHE ASN TYR SEQRES 3 A 468 ALA TRP ALA ARG ARG ASN GLY GLY ARG PHE ILE VAL ARG SEQRES 4 A 468 ILE GLU ASP THR ASP ARG ALA ARG TYR VAL PRO GLY ALA SEQRES 5 A 468 GLU GLU ARG ILE LEU ALA ALA LEU LYS TRP LEU GLY LEU SEQRES 6 A 468 SER TYR ASP GLU GLY PRO ASP VAL GLY GLY PRO HIS GLY SEQRES 7 A 468 PRO TYR ARG GLN SER GLU ARG LEU PRO LEU TYR GLN LYS SEQRES 8 A 468 TYR ALA GLU GLU LEU LEU LYS ARG GLY TRP ALA TYR ARG SEQRES 9 A 468 ALA PHE GLU THR PRO GLU GLU LEU GLU GLN ILE ARG LYS SEQRES 10 A 468 GLU LYS GLY GLY TYR ASP GLY ARG ALA ARG ASN ILE PRO SEQRES 11 A 468 PRO GLU GLU ALA GLU GLU ARG ALA ARG ARG GLY GLU PRO SEQRES 12 A 468 HIS VAL ILE ARG LEU LYS VAL PRO ARG PRO GLY THR THR SEQRES 13 A 468 GLU VAL LYS ASP GLU LEU ARG GLY VAL VAL VAL TYR ASP SEQRES 14 A 468 ASN GLN GLU ILE PRO ASP VAL VAL LEU LEU LYS SER ASP SEQRES 15 A 468 GLY TYR PRO THR TYR HIS LEU ALA ASN VAL VAL ASP ASP SEQRES 16 A 468 HIS LEU MET GLY VAL THR ASP VAL ILE ARG ALA GLU GLU SEQRES 17 A 468 TRP LEU VAL SER THR PRO ILE HIS VAL LEU LEU TYR ARG SEQRES 18 A 468 ALA PHE GLY TRP GLU ALA PRO ARG PHE TYR HIS MET PRO SEQRES 19 A 468 LEU LEU ARG ASN PRO ASP LYS THR LYS ILE SER LYS ARG SEQRES 20 A 468 LYS SER HIS THR SER LEU ASP TRP TYR LYS ALA GLU GLY SEQRES 21 A 468 PHE LEU PRO GLU ALA LEU ARG ASN TYR LEU CYS LEU MET SEQRES 22 A 468 GLY PHE SER MET PRO ASP GLY ARG GLU ILE PHE THR LEU SEQRES 23 A 468 GLU GLU PHE ILE GLN ALA PHE THR TRP GLU ARG VAL SER SEQRES 24 A 468 LEU GLY GLY PRO VAL PHE ASP LEU GLU LYS LEU ARG TRP SEQRES 25 A 468 MET ASN GLY LYS TYR ILE ARG GLU VAL LEU SER LEU GLU SEQRES 26 A 468 GLU VAL ALA GLU ARG VAL LYS PRO PHE LEU ARG GLU ALA SEQRES 27 A 468 GLY LEU SER TRP GLU SER GLU ALA TYR LEU ARG ARG ALA SEQRES 28 A 468 VAL GLU LEU MET ARG PRO ARG PHE ASP THR LEU LYS GLU SEQRES 29 A 468 PHE PRO GLU LYS ALA ARG TYR LEU PHE THR GLU ASP TYR SEQRES 30 A 468 PRO VAL SER GLU LYS ALA GLN ARG LYS LEU GLU GLU GLY SEQRES 31 A 468 LEU PRO LEU LEU LYS GLU LEU TYR PRO ARG LEU ARG ALA SEQRES 32 A 468 GLN GLU GLU TRP THR GLU ALA ALA LEU GLU ALA LEU LEU SEQRES 33 A 468 ARG GLY PHE ALA ALA GLU LYS GLY VAL LYS LEU GLY GLN SEQRES 34 A 468 VAL ALA GLN PRO LEU ARG ALA ALA LEU THR GLY SER LEU SEQRES 35 A 468 GLU THR PRO GLY LEU PHE GLU ILE LEU ALA LEU LEU GLY SEQRES 36 A 468 LYS GLU ARG ALA LEU ARG ARG LEU GLU ARG ALA LEU ALA SEQRES 1 B 468 MET VAL VAL THR ARG ILE ALA PRO SER PRO THR GLY ASP SEQRES 2 B 468 PRO HIS VAL GLY THR ALA TYR ILE ALA LEU PHE ASN TYR SEQRES 3 B 468 ALA TRP ALA ARG ARG ASN GLY GLY ARG PHE ILE VAL ARG SEQRES 4 B 468 ILE GLU ASP THR ASP ARG ALA ARG TYR VAL PRO GLY ALA SEQRES 5 B 468 GLU GLU ARG ILE LEU ALA ALA LEU LYS TRP LEU GLY LEU SEQRES 6 B 468 SER TYR ASP GLU GLY PRO ASP VAL GLY GLY PRO HIS GLY SEQRES 7 B 468 PRO TYR ARG GLN SER GLU ARG LEU PRO LEU TYR GLN LYS SEQRES 8 B 468 TYR ALA GLU GLU LEU LEU LYS ARG GLY TRP ALA TYR ARG SEQRES 9 B 468 ALA PHE GLU THR PRO GLU GLU LEU GLU GLN ILE ARG LYS SEQRES 10 B 468 GLU LYS GLY GLY TYR ASP GLY ARG ALA ARG ASN ILE PRO SEQRES 11 B 468 PRO GLU GLU ALA GLU GLU ARG ALA ARG ARG GLY GLU PRO SEQRES 12 B 468 HIS VAL ILE ARG LEU LYS VAL PRO ARG PRO GLY THR THR SEQRES 13 B 468 GLU VAL LYS ASP GLU LEU ARG GLY VAL VAL VAL TYR ASP SEQRES 14 B 468 ASN GLN GLU ILE PRO ASP VAL VAL LEU LEU LYS SER ASP SEQRES 15 B 468 GLY TYR PRO THR TYR HIS LEU ALA ASN VAL VAL ASP ASP SEQRES 16 B 468 HIS LEU MET GLY VAL THR ASP VAL ILE ARG ALA GLU GLU SEQRES 17 B 468 TRP LEU VAL SER THR PRO ILE HIS VAL LEU LEU TYR ARG SEQRES 18 B 468 ALA PHE GLY TRP GLU ALA PRO ARG PHE TYR HIS MET PRO SEQRES 19 B 468 LEU LEU ARG ASN PRO ASP LYS THR LYS ILE SER LYS ARG SEQRES 20 B 468 LYS SER HIS THR SER LEU ASP TRP TYR LYS ALA GLU GLY SEQRES 21 B 468 PHE LEU PRO GLU ALA LEU ARG ASN TYR LEU CYS LEU MET SEQRES 22 B 468 GLY PHE SER MET PRO ASP GLY ARG GLU ILE PHE THR LEU SEQRES 23 B 468 GLU GLU PHE ILE GLN ALA PHE THR TRP GLU ARG VAL SER SEQRES 24 B 468 LEU GLY GLY PRO VAL PHE ASP LEU GLU LYS LEU ARG TRP SEQRES 25 B 468 MET ASN GLY LYS TYR ILE ARG GLU VAL LEU SER LEU GLU SEQRES 26 B 468 GLU VAL ALA GLU ARG VAL LYS PRO PHE LEU ARG GLU ALA SEQRES 27 B 468 GLY LEU SER TRP GLU SER GLU ALA TYR LEU ARG ARG ALA SEQRES 28 B 468 VAL GLU LEU MET ARG PRO ARG PHE ASP THR LEU LYS GLU SEQRES 29 B 468 PHE PRO GLU LYS ALA ARG TYR LEU PHE THR GLU ASP TYR SEQRES 30 B 468 PRO VAL SER GLU LYS ALA GLN ARG LYS LEU GLU GLU GLY SEQRES 31 B 468 LEU PRO LEU LEU LYS GLU LEU TYR PRO ARG LEU ARG ALA SEQRES 32 B 468 GLN GLU GLU TRP THR GLU ALA ALA LEU GLU ALA LEU LEU SEQRES 33 B 468 ARG GLY PHE ALA ALA GLU LYS GLY VAL LYS LEU GLY GLN SEQRES 34 B 468 VAL ALA GLN PRO LEU ARG ALA ALA LEU THR GLY SER LEU SEQRES 35 B 468 GLU THR PRO GLY LEU PHE GLU ILE LEU ALA LEU LEU GLY SEQRES 36 B 468 LYS GLU ARG ALA LEU ARG ARG LEU GLU ARG ALA LEU ALA HET MG C 700 1 HET MG D 701 1 HET GOM A 600 31 HET GOM B 601 31 HETNAM MG MAGNESIUM ION HETNAM GOM GLUTAMOL-AMP FORMUL 5 MG 2(MG 2+) FORMUL 7 GOM 2(C15 H22 N6 O9 P 1-) FORMUL 9 HOH *751(H2 O) HELIX 1 1 HIS A 15 ASN A 32 1 18 HELIX 2 2 GLY A 51 LEU A 63 1 13 HELIX 3 3 ARG A 81 GLU A 84 5 4 HELIX 4 4 ARG A 85 ARG A 99 1 15 HELIX 5 5 THR A 108 GLY A 120 1 13 HELIX 6 6 GLY A 124 ILE A 129 5 6 HELIX 7 7 PRO A 130 ARG A 140 1 11 HELIX 8 8 GLN A 171 ILE A 173 5 3 HELIX 9 9 THR A 186 MET A 198 1 13 HELIX 10 10 GLU A 208 VAL A 211 5 4 HELIX 11 11 SER A 212 GLY A 224 1 13 HELIX 12 12 SER A 252 GLU A 259 1 8 HELIX 13 13 LEU A 262 LEU A 272 1 11 HELIX 14 14 THR A 285 PHE A 293 1 9 HELIX 15 15 THR A 294 VAL A 298 5 5 HELIX 16 16 ASP A 306 VAL A 321 1 16 HELIX 17 17 SER A 323 ALA A 338 1 16 HELIX 18 18 SER A 344 ARG A 356 1 13 HELIX 19 19 PRO A 357 PHE A 359 5 3 HELIX 20 20 LYS A 363 ALA A 369 1 7 HELIX 21 21 ARG A 370 PHE A 373 5 4 HELIX 22 22 SER A 380 GLY A 390 1 11 HELIX 23 23 GLY A 390 GLN A 404 1 15 HELIX 24 24 THR A 408 LYS A 423 1 16 HELIX 25 25 LEU A 427 GLY A 440 1 14 HELIX 26 26 GLY A 446 LEU A 454 1 9 HELIX 27 27 LEU A 454 ALA A 468 1 15 HELIX 28 28 HIS B 15 ASN B 32 1 18 HELIX 29 29 GLY B 51 LEU B 63 1 13 HELIX 30 30 ARG B 81 GLU B 84 5 4 HELIX 31 31 ARG B 85 ARG B 99 1 15 HELIX 32 32 THR B 108 LYS B 119 1 12 HELIX 33 33 GLY B 124 ASN B 128 5 5 HELIX 34 34 PRO B 130 ARG B 140 1 11 HELIX 35 35 GLN B 171 ILE B 173 5 3 HELIX 36 36 THR B 186 MET B 198 1 13 HELIX 37 37 GLU B 208 VAL B 211 5 4 HELIX 38 38 SER B 212 GLY B 224 1 13 HELIX 39 39 SER B 252 GLU B 259 1 8 HELIX 40 40 LEU B 262 LEU B 272 1 11 HELIX 41 41 THR B 285 PHE B 293 1 9 HELIX 42 42 THR B 294 VAL B 298 5 5 HELIX 43 43 ASP B 306 VAL B 321 1 16 HELIX 44 44 SER B 323 ALA B 338 1 16 HELIX 45 45 SER B 344 ARG B 356 1 13 HELIX 46 46 PRO B 357 PHE B 359 5 3 HELIX 47 47 LYS B 363 ALA B 369 1 7 HELIX 48 48 ARG B 370 PHE B 373 5 4 HELIX 49 49 SER B 380 GLY B 390 1 11 HELIX 50 50 GLY B 390 GLN B 404 1 15 HELIX 51 51 THR B 408 LYS B 423 1 16 HELIX 52 52 LYS B 426 GLY B 440 1 15 HELIX 53 53 GLY B 446 LEU B 454 1 9 HELIX 54 54 GLY B 455 ALA B 468 1 14 SHEET 1 A 2 VAL A 3 ILE A 6 0 SHEET 2 A 2 ARG A 35 VAL A 38 1 O ILE A 37 N THR A 4 SHEET 1 B 3 ALA A 102 ALA A 105 0 SHEET 2 B 3 VAL A 145 LEU A 148 -1 O ARG A 147 N TYR A 103 SHEET 3 B 3 VAL A 177 LEU A 179 -1 O LEU A 178 N ILE A 146 SHEET 1 C 2 THR A 155 ASP A 160 0 SHEET 2 C 2 GLY A 164 ASP A 169 -1 O TYR A 168 N THR A 156 SHEET 1 D 2 ASP A 202 ALA A 206 0 SHEET 2 D 2 ARG A 229 MET A 233 1 O ARG A 229 N VAL A 203 SHEET 1 E 2 VAL B 3 ILE B 6 0 SHEET 2 E 2 ARG B 35 VAL B 38 1 O ILE B 37 N THR B 4 SHEET 1 F 3 ALA B 102 ALA B 105 0 SHEET 2 F 3 VAL B 145 LEU B 148 -1 O VAL B 145 N ALA B 105 SHEET 3 F 3 VAL B 177 LEU B 179 -1 O LEU B 178 N ILE B 146 SHEET 1 G 2 THR B 155 ASP B 160 0 SHEET 2 G 2 GLY B 164 ASP B 169 -1 O VAL B 166 N VAL B 158 SHEET 1 H 2 ASP B 202 ALA B 206 0 SHEET 2 H 2 ARG B 229 MET B 233 1 O ARG B 229 N VAL B 203 LINK MG MG C 700 O HOH C2317 1555 1555 2.20 LINK MG MG C 700 O HOH C2318 1555 1555 2.44 LINK MG MG C 700 O HOH C2319 1555 1555 1.81 LINK MG MG C 700 O HOH C2320 1555 1555 1.92 LINK MG MG C 700 O HOH C2321 1555 1555 2.09 LINK MG MG C 700 O HOH C2322 1555 1555 2.09 LINK MG MG D 701 O HOH D2323 1555 1555 1.96 LINK MG MG D 701 O HOH D2324 1555 1555 1.91 LINK MG MG D 701 O HOH D2325 1555 1555 2.06 LINK MG MG D 701 O HOH D2326 1555 1555 2.04 LINK MG MG D 701 O HOH D2327 1555 1555 2.11 LINK MG MG D 701 O HOH D2328 1555 1555 2.00 CISPEP 1 GLY A 78 PRO A 79 0 0.05 CISPEP 2 ARG A 152 PRO A 153 0 -0.18 CISPEP 3 GLY B 78 PRO B 79 0 -0.21 CISPEP 4 ARG B 152 PRO B 153 0 0.25 SITE 1 AC1 6 HOH C2317 HOH C2318 HOH C2319 HOH C2320 SITE 2 AC1 6 HOH C2321 HOH C2322 SITE 1 AC2 6 HOH D2323 HOH D2324 HOH D2325 HOH D2326 SITE 2 AC2 6 HOH D2327 HOH D2328 SITE 1 AC3 22 ARG A 5 ALA A 7 PRO A 8 SER A 9 SITE 2 AC3 22 GLY A 17 THR A 18 ILE A 21 GLU A 41 SITE 3 AC3 22 TYR A 187 ASN A 191 ARG A 205 ALA A 206 SITE 4 AC3 22 GLU A 208 TRP A 209 LEU A 235 LEU A 236 SITE 5 AC3 22 ILE A 244 HOH A1122 HOH A1294 HOH A1360 SITE 6 AC3 22 HOH A1480 A C 576 SITE 1 AC4 20 ARG B 5 ALA B 7 SER B 9 GLY B 17 SITE 2 AC4 20 THR B 18 ILE B 21 GLU B 41 TYR B 187 SITE 3 AC4 20 ASN B 191 ARG B 205 ALA B 206 GLU B 208 SITE 4 AC4 20 TRP B 209 LEU B 235 LEU B 236 ILE B 244 SITE 5 AC4 20 HOH B1137 HOH B1256 HOH B1624 A D 576 CRYST1 110.492 219.870 135.119 90.00 90.00 90.00 C 2 2 21 16 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 0.009050 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007401 0.00000