HEADER LIGASE 29-APR-20 6WRN TITLE CRYSTAL STRUCTURE OF MJ 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) C70A TITLE 2 VARIANT BOUND TO 3-NITRO-TYROSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TYROSYL-TRNA SYNTHETASE,TYRRS; COMPND 5 EC: 6.1.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII (STRAIN ATCC SOURCE 3 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440); SOURCE 4 ORGANISM_TAXID: 243232; SOURCE 5 STRAIN: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440; SOURCE 6 GENE: TYRS, MJ0389; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS AMINOACYL-TRNA SYNTHETASE, 3-NITRO-TYROSINE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.N.BEYER,P.HOSSEINZADEH,P.A.KARPLUS,R.A.MEHL,R.B.COOLEY REVDAT 3 18-OCT-23 6WRN 1 REMARK REVDAT 2 05-AUG-20 6WRN 1 JRNL REVDAT 1 01-JUL-20 6WRN 0 JRNL AUTH J.N.BEYER,P.HOSSEINZADEH,I.GOTTFRIED-LEE,E.M.VAN FOSSEN, JRNL AUTH 2 P.ZHU,R.M.BEDNAR,P.A.KARPLUS,R.A.MEHL,R.B.COOLEY JRNL TITL OVERCOMING NEAR-COGNATE SUPPRESSION IN A RELEASE FACTOR JRNL TITL 2 1-DEFICIENT HOST WITH AN IMPROVED NITRO-TYROSINE TRNA JRNL TITL 3 SYNTHETASE. JRNL REF J.MOL.BIOL. V. 432 4690 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 32569745 JRNL DOI 10.1016/J.JMB.2020.06.014 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1-3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 50245 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.5700 - 3.8600 1.00 3702 154 0.1680 0.2039 REMARK 3 2 3.8500 - 3.0600 1.00 3542 146 0.1592 0.1866 REMARK 3 3 3.0600 - 2.6700 1.00 3478 145 0.1719 0.1766 REMARK 3 4 2.6700 - 2.4300 1.00 3472 143 0.1745 0.2087 REMARK 3 5 2.4300 - 2.2600 1.00 3450 143 0.1734 0.2005 REMARK 3 6 2.2500 - 2.1200 1.00 3418 142 0.1820 0.2097 REMARK 3 7 2.1200 - 2.0200 1.00 3438 141 0.1969 0.2694 REMARK 3 8 2.0200 - 1.9300 1.00 3409 140 0.2160 0.2696 REMARK 3 9 1.9300 - 1.8500 1.00 3403 142 0.2376 0.2409 REMARK 3 10 1.8500 - 1.7900 1.00 3409 142 0.2442 0.2782 REMARK 3 11 1.7900 - 1.7300 0.99 3372 139 0.2657 0.2713 REMARK 3 12 1.7300 - 1.6800 0.99 3398 140 0.2919 0.3217 REMARK 3 13 1.6800 - 1.6400 0.99 3375 140 0.3301 0.3340 REMARK 3 14 1.6400 - 1.6000 0.99 3382 140 0.3695 0.4049 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.231 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.808 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.017 2698 REMARK 3 ANGLE : 1.427 3641 REMARK 3 CHIRALITY : 0.098 397 REMARK 3 PLANARITY : 0.009 473 REMARK 3 DIHEDRAL : 24.431 1074 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6WRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000248904. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9-8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50272 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 41.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 30.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 30.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4NDA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-23% PEG 300, 5% PEG 8000, 10% REMARK 280 GLYCEROL AND 100 MM TRIS PH 7.9-8.2, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 35.74000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.09500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.61000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.09500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.09500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.87000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.09500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.09500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.61000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.09500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.09500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.87000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 35.74000 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: 2960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 0.000000 -1.000000 0.000000 102.19000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 102.19000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -35.74000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 542 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 774 LIES ON A SPECIAL POSITION. 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 HIS A 313 REMARK 465 HIS A 314 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 312 CG ND1 CD2 CE1 NE2 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 HZ1 LYS A 228 O HOH A 501 1.40 REMARK 500 OE2 GLU A 220 HH11 ARG A 223 1.55 REMARK 500 OD1 ASP A 87 OH TYR A 104 1.85 REMARK 500 NZ LYS A 228 O HOH A 501 2.02 REMARK 500 O LYS A 76 O HOH A 502 2.07 REMARK 500 OD1 ASP A 27 O HOH A 503 2.10 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 764 O HOH A 764 8665 1.99 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 ARG A 21 N ARG A 21 CA 0.133 REMARK 500 ARG A 21 CZ ARG A 21 NH1 0.089 REMARK 500 ARG A 21 CZ ARG A 21 NH2 0.090 REMARK 500 ARG A 21 CA ARG A 21 C 0.163 REMARK 500 ARG A 129 CZ ARG A 129 NH1 0.084 REMARK 500 GLU A 142 N GLU A 142 CA 0.143 REMARK 500 ILE A 153 C MET A 154 N 0.212 REMARK 500 SER A 158 CB SER A 158 OG -0.099 REMARK 500 ARG A 181 CZ ARG A 181 NH2 0.080 REMARK 500 LYS A 304 N LYS A 304 CA 0.123 REMARK 500 LYS A 304 CA LYS A 304 C 0.159 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 ILE A 153 CA - C - O ANGL. DEV. = 15.5 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 GLN A 75 33.94 70.83 REMARK 500 CYS A 231 67.61 -167.18 REMARK 500 HIS A 311 -12.73 126.96 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 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 27 OD2 REMARK 620 2 PRO A 144 O 14.7 REMARK 620 3 HOH A 739 O 101.6 93.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NIY A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6WRK RELATED DB: PDB REMARK 900 RELATED ID: 6WRT RELATED DB: PDB REMARK 900 RELATED ID: 6WRQ RELATED DB: PDB REMARK 900 RELATED ID: 4NDA RELATED DB: PDB REMARK 900 4NDA CONTAINS THE PARENT 2ND GEN. "5B" SYNTHETASE THAT 6WRN WAS REMARK 900 EVOLVED FROM. 6WRN HAS AN A AT RESIDUE 70, WHERE 4NDA HAS A C. DBREF 6WRN A 1 306 UNP Q57834 SYY_METJA 1 306 SEQADV 6WRN HIS A 32 UNP Q57834 TYR 32 ENGINEERED MUTATION SEQADV 6WRN ALA A 70 UNP Q57834 HIS 70 ENGINEERED MUTATION SEQADV 6WRN SER A 158 UNP Q57834 ASP 158 ENGINEERED MUTATION SEQADV 6WRN ALA A 159 UNP Q57834 ILE 159 ENGINEERED MUTATION SEQADV 6WRN ARG A 162 UNP Q57834 LEU 162 ENGINEERED MUTATION SEQADV 6WRN LEU A 307 UNP Q57834 EXPRESSION TAG SEQADV 6WRN GLU A 308 UNP Q57834 EXPRESSION TAG SEQADV 6WRN HIS A 309 UNP Q57834 EXPRESSION TAG SEQADV 6WRN HIS A 310 UNP Q57834 EXPRESSION TAG SEQADV 6WRN HIS A 311 UNP Q57834 EXPRESSION TAG SEQADV 6WRN HIS A 312 UNP Q57834 EXPRESSION TAG SEQADV 6WRN HIS A 313 UNP Q57834 EXPRESSION TAG SEQADV 6WRN HIS A 314 UNP Q57834 EXPRESSION TAG SEQRES 1 A 314 MET ASP GLU PHE GLU MET ILE LYS ARG ASN THR SER GLU SEQRES 2 A 314 ILE ILE SER GLU GLU GLU LEU ARG GLU VAL LEU LYS LYS SEQRES 3 A 314 ASP GLU LYS SER ALA HIS ILE GLY PHE GLU PRO SER GLY SEQRES 4 A 314 LYS ILE HIS LEU GLY HIS TYR LEU GLN ILE LYS LYS MET SEQRES 5 A 314 ILE ASP LEU GLN ASN ALA GLY PHE ASP ILE ILE ILE LEU SEQRES 6 A 314 LEU ALA ASP LEU ALA ALA TYR LEU ASN GLN LYS GLY GLU SEQRES 7 A 314 LEU ASP GLU ILE ARG LYS ILE GLY ASP TYR ASN LYS LYS SEQRES 8 A 314 VAL PHE GLU ALA MET GLY LEU LYS ALA LYS TYR VAL TYR SEQRES 9 A 314 GLY SER GLU PHE GLN LEU ASP LYS ASP TYR THR LEU ASN SEQRES 10 A 314 VAL TYR ARG LEU ALA LEU LYS THR THR LEU LYS ARG ALA SEQRES 11 A 314 ARG ARG SER MET GLU LEU ILE ALA ARG GLU ASP GLU ASN SEQRES 12 A 314 PRO LYS VAL ALA GLU VAL ILE TYR PRO ILE MET GLN VAL SEQRES 13 A 314 ASN SER ALA HIS TYR ARG GLY VAL ASP VAL ALA VAL GLY SEQRES 14 A 314 GLY MET GLU GLN ARG LYS ILE HIS MET LEU ALA ARG GLU SEQRES 15 A 314 LEU LEU PRO LYS LYS VAL VAL CYS ILE HIS ASN PRO VAL SEQRES 16 A 314 LEU THR GLY LEU ASP GLY GLU GLY LYS MET SER SER SER SEQRES 17 A 314 LYS GLY ASN PHE ILE ALA VAL ASP ASP SER PRO GLU GLU SEQRES 18 A 314 ILE ARG ALA LYS ILE LYS LYS ALA TYR CYS PRO ALA GLY SEQRES 19 A 314 VAL VAL GLU GLY ASN PRO ILE MET GLU ILE ALA LYS TYR SEQRES 20 A 314 PHE LEU GLU TYR PRO LEU THR ILE LYS ARG PRO GLU LYS SEQRES 21 A 314 PHE GLY GLY ASP LEU THR VAL ASN SER TYR GLU GLU LEU SEQRES 22 A 314 GLU SER LEU PHE LYS ASN LYS GLU LEU HIS PRO MET ASP SEQRES 23 A 314 LEU LYS ASN ALA VAL ALA GLU GLU LEU ILE LYS ILE LEU SEQRES 24 A 314 GLU PRO ILE ARG LYS ARG LEU LEU GLU HIS HIS HIS HIS SEQRES 25 A 314 HIS HIS HET NA A 401 1 HET NIY A 402 24 HETNAM NA SODIUM ION HETNAM NIY META-NITRO-TYROSINE FORMUL 2 NA NA 1+ FORMUL 3 NIY C9 H10 N2 O5 FORMUL 4 HOH *278(H2 O) HELIX 1 AA1 ASP A 2 ARG A 9 1 8 HELIX 2 AA2 SER A 16 LYS A 26 1 11 HELIX 3 AA3 HIS A 42 ALA A 58 1 17 HELIX 4 AA4 ALA A 67 ASN A 74 1 8 HELIX 5 AA5 GLU A 78 MET A 96 1 19 HELIX 6 AA6 SER A 106 PHE A 108 5 3 HELIX 7 AA7 ASP A 111 THR A 125 1 15 HELIX 8 AA8 THR A 126 MET A 134 1 9 HELIX 9 AA9 VAL A 146 GLY A 163 1 18 HELIX 10 AB1 GLN A 173 LEU A 184 1 12 HELIX 11 AB2 SER A 218 ALA A 229 1 12 HELIX 12 AB3 ASN A 239 PHE A 248 1 10 HELIX 13 AB4 PRO A 258 GLY A 262 5 5 HELIX 14 AB5 SER A 269 ASN A 279 1 11 HELIX 15 AB6 HIS A 283 HIS A 311 1 29 SHEET 1 AA1 6 GLU A 13 ILE A 15 0 SHEET 2 AA1 6 VAL A 189 ASN A 193 -1 O CYS A 190 N ILE A 15 SHEET 3 AA1 6 VAL A 166 GLY A 170 1 N ALA A 167 O VAL A 189 SHEET 4 AA1 6 SER A 30 PHE A 35 1 N HIS A 32 O VAL A 168 SHEET 5 AA1 6 ASP A 61 LEU A 66 1 O LEU A 65 N ILE A 33 SHEET 6 AA1 6 LYS A 101 TYR A 104 1 O VAL A 103 N LEU A 66 SHEET 1 AA2 2 LEU A 253 ILE A 255 0 SHEET 2 AA2 2 LEU A 265 VAL A 267 -1 O LEU A 265 N ILE A 255 LINK OD2 ASP A 27 NA NA A 401 1555 1555 2.38 LINK O PRO A 144 NA NA A 401 1555 5644 2.78 LINK NA NA A 401 O HOH A 739 1555 5654 2.75 CISPEP 1 ILE A 15 SER A 16 0 -1.91 CISPEP 2 TYR A 251 PRO A 252 0 2.67 SITE 1 AC1 5 ASP A 27 LEU A 127 LYS A 128 PRO A 144 SITE 2 AC1 5 HOH A 739 SITE 1 AC2 16 GLY A 34 PHE A 35 GLU A 36 LEU A 65 SITE 2 AC2 16 ALA A 67 ALA A 70 GLN A 109 TYR A 151 SITE 3 AC2 16 MET A 154 GLN A 155 SER A 158 GLN A 173 SITE 4 AC2 16 HOH A 554 HOH A 565 HOH A 570 HOH A 571 CRYST1 102.190 102.190 71.480 90.00 90.00 90.00 P 43 21 2 8 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 0.009786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009786 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013990 0.00000