PDB Short entry for 2CV1 HEADER LIGASE/RNA 31-MAY-05 2CV1 TITLE GLUTAMYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS IN TITLE 2 COMPLEX WITH TRNA(GLU), ATP, AND AN ANALOG OF L-GLUTAMATE: TITLE 3 A QUATERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA; 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: GLUTAMATE--TRNA LIGASE, GLURS; COMPND 9 EC: 6.1.1.17; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIPTION; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 6 ORGANISM_TAXID: 274; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PK7 KEYWDS LIGASE, RNA, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT KEYWDS 2 ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, LIGASE/RNA KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.SEKINE,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 2 24-FEB-09 2CV1 1 VERSN REVDAT 1 05-SEP-06 2CV1 0 JRNL AUTH S.SEKINE,S.YOKOYAMA JRNL TITL GLUTAMYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS JRNL TITL 2 IN COMPLEX WITH TRNA(GLU), ATP, AND AN ANALOG OF JRNL TITL 3 L-GLUTAMATE: A QUATERNARY COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.41 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3522638.220 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 61079 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) : 0.221 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3087 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6567 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 343 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 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 : 84 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.72000 REMARK 3 B22 (A**2) : -9.27000 REMARK 3 B33 (A**2) : -0.44000 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.36 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.45 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.52 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) : 2.580 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.770 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.840 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.250 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 40.15 REMARK 3 REMARK 3 NCS MODEL : NULL 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 : LIGAND.PARAM REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : 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 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CV1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-05. REMARK 100 THE RCSB ID CODE IS RCSB024651. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-04 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 : BL44XU 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 : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61084 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.09000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 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 : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1500, MOPS-NA, AMMONIUM SULFATE, REMARK 280 MPD, PH 6.7, VAPOR DIFFUSION, 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 67.42900 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 67.42900 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 55.31200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 109.40900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 55.31200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 109.40900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 67.42900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 55.31200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 109.40900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.42900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 55.31200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 109.40900 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: 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 OP2 C D 572 O HOH D 1228 2.14 REMARK 500 OP1 A C 538 O HOH C 1006 2.14 REMARK 500 OP2 U D 520A O HOH D 1227 2.19 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 G C 501 P G C 501 OP3 -0.084 REMARK 500 G D 501 P G D 501 OP3 -0.081 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. = 10.1 DEGREES REMARK 500 G C 519 C2' - C3' - O3' ANGL. DEV. = 12.3 DEGREES REMARK 500 A C 558 C2' - C3' - O3' ANGL. DEV. = 12.7 DEGREES REMARK 500 A C 573 C2' - C3' - O3' ANGL. DEV. = 12.8 DEGREES REMARK 500 C C 574 C2' - C3' - O3' ANGL. DEV. = 11.0 DEGREES REMARK 500 A C 576 C2' - C3' - O3' ANGL. DEV. = 9.8 DEGREES REMARK 500 A D 507 C2' - C3' - O3' ANGL. DEV. = 13.0 DEGREES REMARK 500 G D 518 C2' - C3' - O3' ANGL. DEV. = 11.1 DEGREES REMARK 500 G D 519 C2' - C3' - O3' ANGL. DEV. = 11.3 DEGREES REMARK 500 A D 558 C2' - C3' - O3' ANGL. DEV. = 12.8 DEGREES REMARK 500 A D 573 C2' - C3' - O3' ANGL. DEV. = 11.3 DEGREES REMARK 500 C D 574 C2' - C3' - O3' ANGL. DEV. = 10.0 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 ASP A 42 62.80 -104.11 REMARK 500 LEU A 453 -62.16 -26.16 REMARK 500 PRO B 10 83.84 -69.59 REMARK 500 ASP B 42 44.08 -107.38 REMARK 500 LYS B 241 -4.20 80.03 REMARK 500 LYS B 246 -9.75 -59.38 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 A D 545 0.08 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 D 904 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U D 508 OP2 REMARK 620 2 C D 509 OP2 97.3 REMARK 620 N 1 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 901 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 902 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 903 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 904 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 601 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 602 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAU A 701 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAU A 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G59 RELATED DB: PDB REMARK 900 RELATED ID: 1J09 RELATED DB: PDB REMARK 900 RELATED ID: 1N75 RELATED DB: PDB REMARK 900 RELATED ID: 1N77 RELATED DB: PDB REMARK 900 RELATED ID: 1N78 RELATED DB: PDB REMARK 900 RELATED ID: 2CUZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH L-GLUTAMATE REMARK 900 RELATED ID: 2CV0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH TRNA(GLU), L-GLUTAMATE REMARK 900 RELATED ID: 2CV2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH TRNA(GLU), AN ENZYME REMARK 900 INHIBITOR, GLU-AMS REMARK 900 RELATED ID: TTK003000897.6 RELATED DB: TARGETDB DBREF 2CV1 A 1 468 UNP P27000 SYE_THET8 1 468 DBREF 2CV1 B 1 468 UNP P27000 SYE_THET8 1 468 DBREF 2CV1 C 501 576 PDB 2CV1 2CV1 501 576 DBREF 2CV1 D 501 576 PDB 2CV1 2CV1 501 576 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 901 1 HET MG C 902 1 HET MG D 903 1 HET MG D 904 1 HET ATP A 601 31 HET ATP B 602 31 HET GAU A 701 9 HET GAU A 702 9 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM GAU (4S)-4-AMINO-5-HYDROXYPENTANOIC ACID HETSYN GAU L-GLUTAMOL FORMUL 5 MG 4(MG 2+) FORMUL 9 ATP 2(C10 H16 N5 O13 P3) FORMUL 11 GAU 2(C5 H11 N O3) FORMUL 12 HOH *182(H2 O) HELIX 1 1 HIS A 15 ASN A 32 1 18 HELIX 2 2 GLY A 51 GLY A 64 1 14 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 PHE A 223 1 12 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 GLN A 404 1 25 HELIX 23 23 THR A 408 LYS A 423 1 16 HELIX 24 24 LEU A 427 GLY A 440 1 14 HELIX 25 25 GLY A 446 GLY A 455 1 10 HELIX 26 26 GLY A 455 ALA A 468 1 14 HELIX 27 27 HIS B 15 ASN B 32 1 18 HELIX 28 28 GLY B 51 LEU B 63 1 13 HELIX 29 29 ARG B 81 GLU B 84 5 4 HELIX 30 30 ARG B 85 ARG B 99 1 15 HELIX 31 31 THR B 108 LYS B 119 1 12 HELIX 32 32 GLY B 124 ILE B 129 5 6 HELIX 33 33 PRO B 130 ARG B 140 1 11 HELIX 34 34 GLN B 171 ILE B 173 5 3 HELIX 35 35 THR B 186 MET B 198 1 13 HELIX 36 36 GLU B 208 VAL B 211 5 4 HELIX 37 37 SER B 212 GLY B 224 1 13 HELIX 38 38 SER B 252 GLU B 259 1 8 HELIX 39 39 LEU B 262 MET B 273 1 12 HELIX 40 40 THR B 285 PHE B 293 1 9 HELIX 41 41 THR B 294 VAL B 298 5 5 HELIX 42 42 ASP B 306 VAL B 321 1 16 HELIX 43 43 SER B 323 ALA B 338 1 16 HELIX 44 44 SER B 344 ARG B 356 1 13 HELIX 45 45 PRO B 357 PHE B 359 5 3 HELIX 46 46 LYS B 363 ALA B 369 1 7 HELIX 47 47 ARG B 370 PHE B 373 5 4 HELIX 48 48 SER B 380 GLN B 404 1 25 HELIX 49 49 THR B 408 LYS B 423 1 16 HELIX 50 50 LYS B 426 GLY B 440 1 15 HELIX 51 51 GLY B 446 LEU B 454 1 9 HELIX 52 52 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 VAL A 166 N VAL A 158 SHEET 1 D 2 ASP A 202 ALA A 206 0 SHEET 2 D 2 ARG A 229 MET A 233 1 O TYR A 231 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 ARG B 35 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 ARG B 147 N TYR B 103 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 TYR B 168 N THR B 156 SHEET 1 H 2 ASP B 202 ALA B 206 0 SHEET 2 H 2 ARG B 229 MET B 233 1 O MET B 233 N ARG B 205 LINK MG MG C 901 O HOH C1221 1555 1555 1.99 LINK MG MG C 902 OP2 C C 509 1555 1555 1.91 LINK MG MG D 903 O HOH D1181 1555 1555 2.26 LINK MG MG D 904 OP2 U D 508 1555 1555 2.84 LINK MG MG D 904 OP2 C D 509 1555 1555 2.22 CISPEP 1 GLY A 78 PRO A 79 0 -0.16 CISPEP 2 ARG A 152 PRO A 153 0 -0.33 CISPEP 3 GLY B 78 PRO B 79 0 0.01 CISPEP 4 ARG B 152 PRO B 153 0 -0.37 SITE 1 AC1 2 G C 522 HOH C1221 SITE 1 AC2 2 U C 508 C C 509 SITE 1 AC3 3 C D 509 A D 545 HOH D1181 SITE 1 AC4 3 U D 508 C D 509 C D 512 SITE 1 AC5 15 PRO A 8 SER A 9 THR A 11 HIS A 15 SITE 2 AC5 15 GLY A 17 THR A 18 ILE A 21 ARG A 47 SITE 3 AC5 15 ALA A 206 TRP A 209 LEU A 235 LEU A 236 SITE 4 AC5 15 ILE A 244 GAU A 701 A C 576 SITE 1 AC6 15 GAU A 702 PRO B 8 SER B 9 THR B 11 SITE 2 AC6 15 HIS B 15 GLY B 17 THR B 18 ILE B 21 SITE 3 AC6 15 ARG B 47 ALA B 206 GLU B 208 TRP B 209 SITE 4 AC6 15 LEU B 235 LEU B 236 ILE B 244 SITE 1 AC7 9 ARG A 5 ALA A 7 GLU A 41 TYR A 187 SITE 2 AC7 9 ASN A 191 ARG A 205 TRP A 209 ATP A 601 SITE 3 AC7 9 A C 576 SITE 1 AC8 10 ARG B 5 ALA B 7 SER B 9 GLU B 41 SITE 2 AC8 10 TYR B 187 ASN B 191 ARG B 205 TRP B 209 SITE 3 AC8 10 ATP B 602 A D 576 CRYST1 110.624 218.818 134.858 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 0.009040 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004570 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007415 0.00000