HEADER LIGASE 25-OCT-13 4NDA TITLE CRYSTAL STRUCTURE OF 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) BOUND TO 3- TITLE 2 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; 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); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A 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 4 28-FEB-24 4NDA 1 REMARK SEQADV REVDAT 3 17-JUL-19 4NDA 1 REMARK REVDAT 2 16-APR-14 4NDA 1 JRNL REVDAT 1 19-MAR-14 4NDA 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 41553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2108 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 23.9928 - 4.1856 1.00 2879 157 0.1594 0.1809 REMARK 3 2 4.1856 - 3.3251 1.00 2749 135 0.1429 0.2034 REMARK 3 3 3.3251 - 2.9056 1.00 2666 172 0.1729 0.2154 REMARK 3 4 2.9056 - 2.6403 1.00 2690 136 0.1797 0.2553 REMARK 3 5 2.6403 - 2.4512 1.00 2668 135 0.1747 0.1974 REMARK 3 6 2.4512 - 2.3068 1.00 2667 139 0.1669 0.2085 REMARK 3 7 2.3068 - 2.1914 1.00 2659 134 0.1670 0.2061 REMARK 3 8 2.1914 - 2.0961 1.00 2650 135 0.1718 0.2212 REMARK 3 9 2.0961 - 2.0154 1.00 2643 128 0.1791 0.2354 REMARK 3 10 2.0154 - 1.9459 0.99 2608 155 0.2119 0.2518 REMARK 3 11 1.9459 - 1.8851 0.99 2615 118 0.2195 0.2528 REMARK 3 12 1.8851 - 1.8312 0.98 2589 132 0.2507 0.2947 REMARK 3 13 1.8312 - 1.7830 0.97 2538 145 0.2812 0.2868 REMARK 3 14 1.7830 - 1.7395 0.95 2473 159 0.3380 0.3262 REMARK 3 15 1.7395 - 1.7000 0.89 2351 128 0.3813 0.4177 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.600 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 2655 REMARK 3 ANGLE : 1.041 3578 REMARK 3 CHIRALITY : 0.076 391 REMARK 3 PLANARITY : 0.004 464 REMARK 3 DIHEDRAL : 14.490 1057 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): 76.1550 43.4739 -4.3535 REMARK 3 T TENSOR REMARK 3 T11: 0.0837 T22: -0.0273 REMARK 3 T33: 0.0820 T12: -0.0248 REMARK 3 T13: -0.0187 T23: 0.0190 REMARK 3 L TENSOR REMARK 3 L11: 1.7788 L22: 1.0444 REMARK 3 L33: 3.6711 L12: 0.2425 REMARK 3 L13: 1.1380 L23: 1.0304 REMARK 3 S TENSOR REMARK 3 S11: -0.0678 S12: 0.0324 S13: 0.1361 REMARK 3 S21: -0.0055 S22: -0.0371 S23: 0.0043 REMARK 3 S31: -0.3179 S32: 0.0895 S33: 0.0384 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 195:308) REMARK 3 ORIGIN FOR THE GROUP (A): 86.4857 37.3296 20.8430 REMARK 3 T TENSOR REMARK 3 T11: 0.1226 T22: 0.1254 REMARK 3 T33: 0.0990 T12: -0.0394 REMARK 3 T13: -0.0508 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 2.5693 L22: 2.0056 REMARK 3 L33: 2.7580 L12: -0.2309 REMARK 3 L13: 0.7159 L23: -0.1845 REMARK 3 S TENSOR REMARK 3 S11: -0.0655 S12: -0.1578 S13: 0.0287 REMARK 3 S21: 0.1861 S22: -0.0143 S23: -0.2349 REMARK 3 S31: -0.0941 S32: 0.2179 S33: 0.0382 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 4NDA 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_1000083057. 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 : 5.0.2 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 : DOUBLE-CRYSTAL, SI(111) LIQUID REMARK 200 N2 COOLED REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41621 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 23.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 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) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 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 (%): 52.47 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 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 35.86000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.03500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.03500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.79000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.03500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.03500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.93000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.03500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.03500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.79000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.03500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.03500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.93000 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 35.86000 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: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 102.07000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 102.07000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -35.86000 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 375 HOH A1158 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 309 REMARK 465 HIS A 310 REMARK 465 HIS A 311 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 OH TYR A 104 1.92 REMARK 500 OD1 ASP A 27 O HOH A 1070 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 1085 O HOH A 1285 3644 1.91 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 2 157.32 -34.33 REMARK 500 CYS A 231 69.49 -164.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NIY 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 GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 404 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: 4ND7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APO 3-NITRO-TYROSINE TRNA SYNTHETASE (5B) IN REMARK 900 THE CLOSED FORM DBREF 4NDA A 1 306 UNP Q57834 SYY_METJA 1 306 SEQADV 4NDA HIS A 32 UNP Q57834 TYR 32 ENGINEERED MUTATION SEQADV 4NDA CYS A 70 UNP Q57834 HIS 70 ENGINEERED MUTATION SEQADV 4NDA SER A 158 UNP Q57834 ASP 158 ENGINEERED MUTATION SEQADV 4NDA ALA A 159 UNP Q57834 ILE 159 ENGINEERED MUTATION SEQADV 4NDA ARG A 162 UNP Q57834 LEU 162 ENGINEERED MUTATION SEQADV 4NDA LEU A 307 UNP Q57834 EXPRESSION TAG SEQADV 4NDA GLU A 308 UNP Q57834 EXPRESSION TAG SEQADV 4NDA HIS A 309 UNP Q57834 EXPRESSION TAG SEQADV 4NDA HIS A 310 UNP Q57834 EXPRESSION TAG SEQADV 4NDA HIS A 311 UNP Q57834 EXPRESSION TAG SEQADV 4NDA HIS A 312 UNP Q57834 EXPRESSION TAG SEQADV 4NDA HIS A 313 UNP Q57834 EXPRESSION TAG SEQADV 4NDA 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 NIY A 401 16 HET GOL A 402 6 HET GOL A 403 14 HET NA A 404 1 HETNAM NIY META-NITRO-TYROSINE HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NIY C9 H10 N2 O5 FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 NA NA 1+ FORMUL 6 HOH *300(H2 O) HELIX 1 1 ASP A 2 ARG A 9 1 8 HELIX 2 2 SER A 16 LYS A 25 1 10 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 LEU A 123 1 13 HELIX 8 8 THR A 126 MET A 134 1 9 HELIX 9 9 LYS A 145 ARG A 162 1 18 HELIX 10 10 GLN A 173 LEU A 184 1 12 HELIX 11 11 SER A 206 GLY A 210 5 5 HELIX 12 12 SER A 218 ALA A 229 1 12 HELIX 13 13 ASN A 239 PHE A 248 1 10 HELIX 14 14 PRO A 258 GLY A 262 5 5 HELIX 15 15 SER A 269 ASN A 279 1 11 HELIX 16 16 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 LYS A 101 N ILE A 64 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 404 1555 1555 2.44 CISPEP 1 ILE A 15 SER A 16 0 -4.53 CISPEP 2 ILE A 15 SER A 16 0 -4.04 CISPEP 3 TYR A 251 PRO A 252 0 1.46 SITE 1 AC1 15 GLY A 34 PHE A 35 GLU A 36 LEU A 65 SITE 2 AC1 15 ALA A 67 CYS A 70 GLN A 109 TYR A 151 SITE 3 AC1 15 GLN A 155 SER A 158 GLN A 173 HOH A1002 SITE 4 AC1 15 HOH A1034 HOH A1053 HOH A1059 SITE 1 AC2 4 ARG A 223 ASN A 289 ALA A 292 GLU A 293 SITE 1 AC3 5 LEU A 136 VAL A 195 LYS A 204 HOH A1124 SITE 2 AC3 5 HOH A1250 SITE 1 AC4 6 ASP A 27 THR A 126 LEU A 127 LYS A 128 SITE 2 AC4 6 PRO A 144 HOH A1064 CRYST1 102.070 102.070 71.720 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 0.009797 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009797 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013943 0.00000