HEADER LIGASE 25-OCT-13 4ND7 TITLE CRYSTAL STRUCTURE OF APO 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) IN THE TITLE 2 CLOSED FORM 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; SOURCE 3 ORGANISM_TAXID: 243232; SOURCE 4 STRAIN: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440; SOURCE 5 GENE: MJ0389, TYRS, TYRS MJ0389; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ROSMANN FOLD, 3-NITRO-TYROSINE AMINO-ACYL TRNA SYNTHETASE, TRNA, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR R.B.COOLEY,C.M.DRIGGERS,P.A.KARPLUS,R.A.MEHL REVDAT 3 17-JUL-19 4ND7 1 REMARK LINK REVDAT 2 16-APR-14 4ND7 1 JRNL REVDAT 1 19-MAR-14 4ND7 0 JRNL AUTH R.B.COOLEY,J.L.FELDMAN,C.M.DRIGGERS,T.A.BUNDY,A.L.STOKES, JRNL AUTH 2 P.A.KARPLUS,R.A.MEHL JRNL TITL STRUCTURAL BASIS OF IMPROVED SECOND-GENERATION JRNL TITL 2 3-NITRO-TYROSINE TRNA SYNTHETASES. JRNL REF BIOCHEMISTRY V. 53 1916 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24611875 JRNL DOI 10.1021/BI5001239 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26163 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1327 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 51.0135 - 4.1595 1.00 2981 138 0.2066 0.2338 REMARK 3 2 4.1595 - 3.3017 1.00 2796 147 0.1873 0.2534 REMARK 3 3 3.3017 - 2.8844 1.00 2722 183 0.2349 0.3084 REMARK 3 4 2.8844 - 2.6207 1.00 2769 129 0.2482 0.3157 REMARK 3 5 2.6207 - 2.4328 1.00 2732 140 0.2510 0.3239 REMARK 3 6 2.4328 - 2.2894 1.00 2733 147 0.2621 0.3280 REMARK 3 7 2.2894 - 2.1748 1.00 2709 147 0.2724 0.3494 REMARK 3 8 2.1748 - 2.0801 1.00 2706 142 0.3058 0.3418 REMARK 3 9 2.0801 - 2.0000 1.00 2688 154 0.3412 0.3766 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 2646 REMARK 3 ANGLE : 1.050 3564 REMARK 3 CHIRALITY : 0.070 391 REMARK 3 PLANARITY : 0.005 463 REMARK 3 DIHEDRAL : 13.765 1050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:194) REMARK 3 ORIGIN FOR THE GROUP (A): 75.8970 43.3870 -4.5993 REMARK 3 T TENSOR REMARK 3 T11: 0.1907 T22: 0.1915 REMARK 3 T33: 0.2770 T12: -0.0269 REMARK 3 T13: -0.0725 T23: -0.0593 REMARK 3 L TENSOR REMARK 3 L11: 3.4183 L22: 0.6991 REMARK 3 L33: 6.1808 L12: 0.0800 REMARK 3 L13: 2.9162 L23: 1.1341 REMARK 3 S TENSOR REMARK 3 S11: -0.1327 S12: -0.1868 S13: 0.1724 REMARK 3 S21: 0.0651 S22: -0.1059 S23: 0.2878 REMARK 3 S31: -0.2244 S32: 0.0601 S33: 0.1695 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 195:308) REMARK 3 ORIGIN FOR THE GROUP (A): 86.2550 37.2968 20.6036 REMARK 3 T TENSOR REMARK 3 T11: 0.2534 T22: 0.4044 REMARK 3 T33: 0.2136 T12: -0.0748 REMARK 3 T13: -0.0554 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 3.1545 L22: 3.3486 REMARK 3 L33: 5.3729 L12: -0.4167 REMARK 3 L13: 0.2970 L23: -0.8991 REMARK 3 S TENSOR REMARK 3 S11: -0.1512 S12: -0.2283 S13: -0.0889 REMARK 3 S21: 0.1905 S22: 0.0646 S23: -0.1398 REMARK 3 S31: 0.2227 S32: -0.0756 S33: 0.0320 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 4ND7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000083054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 8.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK SI(111) SAGITALLY REMARK 200 FOCUSED MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26163 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 51.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.56 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 8.0 TO 8.3, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K, PH 8.1 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 36.14000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.88500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.21000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.88500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.88500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.07000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.88500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.88500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 54.21000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.88500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.88500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 18.07000 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 36.14000 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: 3470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 101.77000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 101.77000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -36.14000 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 A1009 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 311 REMARK 465 HIS A 312 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 310 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 OD1 ASP A 27 O HOH A 1071 2.11 REMARK 500 O HOH A 1126 O HOH A 1131 2.16 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 OE2 GLU A 221 O HOH A 1043 8665 2.13 REMARK 500 OE2 GLU A 221 O HOH A 1058 8665 2.16 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 2 158.14 -47.29 REMARK 500 CYS A 231 71.76 -168.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 BME A 402 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 HOH A1103 O 98.0 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 NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ND6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APO 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) IN REMARK 900 THE OPEN FORM REMARK 900 RELATED ID: 4NDA RELATED DB: PDB DBREF 4ND7 A 1 306 UNP Q57834 SYY_METJA 1 306 SEQADV 4ND7 HIS A 32 UNP Q57834 TYR 32 ENGINEERED MUTATION SEQADV 4ND7 CYS A 70 UNP Q57834 HIS 70 ENGINEERED MUTATION SEQADV 4ND7 SER A 158 UNP Q57834 ASP 158 ENGINEERED MUTATION SEQADV 4ND7 ALA A 159 UNP Q57834 ILE 159 ENGINEERED MUTATION SEQADV 4ND7 ARG A 162 UNP Q57834 LEU 162 ENGINEERED MUTATION SEQADV 4ND7 LEU A 307 UNP Q57834 EXPRESSION TAG SEQADV 4ND7 GLU A 308 UNP Q57834 EXPRESSION TAG SEQADV 4ND7 HIS A 309 UNP Q57834 EXPRESSION TAG SEQADV 4ND7 HIS A 310 UNP Q57834 EXPRESSION TAG SEQADV 4ND7 HIS A 311 UNP Q57834 EXPRESSION TAG SEQADV 4ND7 HIS A 312 UNP Q57834 EXPRESSION TAG SEQADV 4ND7 HIS A 313 UNP Q57834 EXPRESSION TAG SEQADV 4ND7 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 CYS 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 BME A 402 2 HETNAM NA SODIUM ION HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 NA NA 1+ FORMUL 3 BME C2 H6 O S FORMUL 4 HOH *134(H2 O) HELIX 1 1 ASP A 2 ARG A 9 1 8 HELIX 2 2 SER A 16 LYS A 26 1 11 HELIX 3 3 HIS A 42 ALA A 58 1 17 HELIX 4 4 ALA A 67 ASN A 74 1 8 HELIX 5 5 GLU A 78 MET A 96 1 19 HELIX 6 6 SER A 106 PHE A 108 5 3 HELIX 7 7 ASP A 111 THR A 125 1 15 HELIX 8 8 THR A 126 MET A 134 1 9 HELIX 9 9 LYS A 145 GLY A 163 1 19 HELIX 10 10 GLN A 173 LEU A 184 1 12 HELIX 11 11 SER A 218 ALA A 229 1 12 HELIX 12 12 ASN A 239 LEU A 249 1 11 HELIX 13 13 PRO A 258 GLY A 262 5 5 HELIX 14 14 SER A 269 ASN A 279 1 11 HELIX 15 15 HIS A 283 GLU A 308 1 26 SHEET 1 A 6 GLU A 13 ILE A 15 0 SHEET 2 A 6 VAL A 189 ASN A 193 -1 O CYS A 190 N ILE A 15 SHEET 3 A 6 VAL A 166 GLY A 170 1 N ALA A 167 O VAL A 189 SHEET 4 A 6 SER A 30 PHE A 35 1 N HIS A 32 O VAL A 168 SHEET 5 A 6 ASP A 61 LEU A 66 1 O LEU A 65 N ILE A 33 SHEET 6 A 6 LYS A 101 TYR A 104 1 O VAL A 103 N LEU A 66 SHEET 1 B 2 LEU A 253 ILE A 255 0 SHEET 2 B 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 2.43 LINK NA NA A 401 O HOH A1103 1555 1555 2.74 LINK SG CYS A 70 S2 BME A 402 1555 1555 2.07 CISPEP 1 ILE A 15 SER A 16 0 -5.39 CISPEP 2 ILE A 15 SER A 16 0 -3.48 CISPEP 3 TYR A 251 PRO A 252 0 2.36 SITE 1 AC1 5 ASP A 27 LEU A 127 LYS A 128 PRO A 144 SITE 2 AC1 5 HOH A1103 SITE 1 AC2 3 CYS A 70 TYR A 151 GLN A 155 CRYST1 101.770 101.770 72.280 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 0.009826 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013835 0.00000