HEADER LIGASE 29-APR-20 6WRK TITLE CRYSTAL STRUCTURE OF 3RD-GENERATION MJ 3-NITRO-TYROSINE TRNA TITLE 2 SYNTHETASE ("A7") 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; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 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 6WRK 1 REMARK REVDAT 2 05-AUG-20 6WRK 1 JRNL REVDAT 1 01-JUL-20 6WRK 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. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 27735 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.960 REMARK 3 FREE R VALUE TEST SET COUNT : 821 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 45.3600 - 3.5400 1.00 4710 144 0.1608 0.1652 REMARK 3 2 3.5400 - 2.8100 1.00 4507 137 0.1608 0.2180 REMARK 3 3 2.8100 - 2.4600 1.00 4467 136 0.1769 0.1942 REMARK 3 4 2.4600 - 2.2300 1.00 4430 135 0.2020 0.2671 REMARK 3 5 2.2300 - 2.0700 1.00 4409 135 0.2442 0.2472 REMARK 3 6 2.0700 - 1.9500 1.00 4391 134 0.3229 0.3780 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) : 0.281 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.527 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.99 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 2733 REMARK 3 ANGLE : 1.564 3687 REMARK 3 CHIRALITY : 0.100 399 REMARK 3 PLANARITY : 0.012 480 REMARK 3 DIHEDRAL : 25.580 1085 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 6WRK 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_1000248880. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-19 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 : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28169 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 45.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 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 (%): 51.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-23% PEG 300, 5% PEG 8000, 10% REMARK 280 GLYCEROL AND 100 MM TRIS PH 7.9 TO 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 35.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.71500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.71500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.62500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.71500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.71500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.87500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.71500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.71500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.62500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.71500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.71500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.87500 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 35.75000 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: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 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 101.43000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 101.43000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -35.75000 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 529 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 312 REMARK 465 HIS A 313 REMARK 465 HIS A 314 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 OD1 ASP A 87 HH TYR A 104 1.56 REMARK 500 OD1 ASP A 87 OH TYR A 104 1.94 REMARK 500 OG SER A 206 OH NIY A 405 2.14 REMARK 500 OE2 GLU A 78 O HOH A 501 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 MET A 1 HH12 ARG A 174 4565 1.37 REMARK 500 O HOH A 622 O HOH A 623 8665 2.11 REMARK 500 O MET A 1 NH1 ARG A 174 4565 2.14 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 9 CZ ARG A 9 NH1 0.089 REMARK 500 ARG A 9 CZ ARG A 9 NH2 0.086 REMARK 500 ARG A 9 CZ ARG A 9 NH2 0.089 REMARK 500 ARG A 9 CA ARG A 9 C 0.164 REMARK 500 GLU A 78 N GLU A 78 CA 0.121 REMARK 500 ARG A 257 CZ ARG A 257 NH1 0.081 REMARK 500 ARG A 257 CZ ARG A 257 NH2 0.079 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 9 CA - CB - CG ANGL. DEV. = 16.5 DEGREES REMARK 500 ARG A 9 CA - C - N ANGL. DEV. = -14.4 DEGREES REMARK 500 GLU A 78 N - CA - C ANGL. DEV. = 17.4 DEGREES REMARK 500 GLU A 78 CA - C - O ANGL. DEV. = 12.7 DEGREES REMARK 500 ASP A 286 CB - CG - OD2 ANGL. DEV. = 6.0 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 ARG A 9 132.25 -31.18 REMARK 500 GLU A 78 153.24 -46.32 REMARK 500 CYS A 231 72.24 -166.06 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 ARG A 9 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ARG A 9 -17.18 REMARK 500 ARG A 9 -14.73 REMARK 500 ASN A 117 10.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 655 DISTANCE = 8.69 ANGSTROMS 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 27 OD2 REMARK 620 2 PRO A 144 O 18.1 REMARK 620 3 HOH A 649 O 110.3 92.2 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 GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NIY A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NIY A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6WRT RELATED DB: PDB REMARK 900 RELATED ID: 6WRQ RELATED DB: PDB REMARK 900 RELATED ID: 6WRN RELATED DB: PDB REMARK 900 RELATED ID: 4NDA RELATED DB: PDB REMARK 900 4NDA IS THE 2ND GEN. "5B" PARENT SYNTHETASE DBREF 6WRK A 1 306 UNP Q57834 SYY_METJA 1 306 SEQADV 6WRK HIS A 32 UNP Q57834 TYR 32 ENGINEERED MUTATION SEQADV 6WRK THR A 70 UNP Q57834 HIS 70 ENGINEERED MUTATION SEQADV 6WRK HIS A 158 UNP Q57834 ASP 158 ENGINEERED MUTATION SEQADV 6WRK ALA A 159 UNP Q57834 ILE 159 ENGINEERED MUTATION SEQADV 6WRK ARG A 162 UNP Q57834 LEU 162 ENGINEERED MUTATION SEQADV 6WRK LEU A 307 UNP Q57834 EXPRESSION TAG SEQADV 6WRK GLU A 308 UNP Q57834 EXPRESSION TAG SEQADV 6WRK HIS A 309 UNP Q57834 EXPRESSION TAG SEQADV 6WRK HIS A 310 UNP Q57834 EXPRESSION TAG SEQADV 6WRK HIS A 311 UNP Q57834 EXPRESSION TAG SEQADV 6WRK HIS A 312 UNP Q57834 EXPRESSION TAG SEQADV 6WRK HIS A 313 UNP Q57834 EXPRESSION TAG SEQADV 6WRK 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 THR 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 HIS 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 GOL A 401 14 HET GOL A 402 12 HET NA A 403 1 HET NIY A 404 24 HET NIY A 405 25 HET GOL A 406 14 HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETNAM NIY META-NITRO-TYROSINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 4 NA NA 1+ FORMUL 5 NIY 2(C9 H10 N2 O5) FORMUL 8 HOH *155(H2 O) HELIX 1 AA1 ASP A 2 ARG A 9 1 8 HELIX 2 AA2 SER A 16 LYS A 25 1 10 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 LEU A 123 1 13 HELIX 8 AA8 THR A 126 MET A 134 1 9 HELIX 9 AA9 LYS A 145 GLY A 163 1 19 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 LYS A 29 PHE A 35 1 N HIS A 32 O VAL A 168 SHEET 5 AA1 6 PHE A 60 LEU A 66 1 O ASP A 61 N LYS A 29 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 403 1555 1555 2.42 LINK O PRO A 144 NA NA A 403 1555 5644 2.73 LINK NA NA A 403 O HOH A 649 1555 4565 3.03 CISPEP 1 ILE A 15 SER A 16 0 -9.55 CISPEP 2 ILE A 15 SER A 16 0 -8.76 CISPEP 3 TYR A 251 PRO A 252 0 5.91 SITE 1 AC1 5 ARG A 223 LYS A 227 MET A 285 ASN A 289 SITE 2 AC1 5 GLU A 293 SITE 1 AC2 2 VAL A 195 HOH A 503 SITE 1 AC3 6 ASP A 27 THR A 126 LEU A 127 LYS A 128 SITE 2 AC3 6 PRO A 144 HOH A 649 SITE 1 AC4 14 GLY A 34 GLU A 36 LEU A 65 ALA A 67 SITE 2 AC4 14 THR A 70 GLN A 109 TYR A 151 MET A 154 SITE 3 AC4 14 GLN A 155 HIS A 158 GLN A 173 HOH A 541 SITE 4 AC4 14 HOH A 557 HOH A 571 SITE 1 AC5 10 LYS A 76 GLU A 135 ALA A 138 ARG A 139 SITE 2 AC5 10 GLU A 140 LYS A 204 SER A 206 SER A 208 SITE 3 AC5 10 HOH A 505 HOH A 575 SITE 1 AC6 1 GLU A 94 CRYST1 101.430 101.430 71.500 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 0.009859 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009859 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013986 0.00000