HEADER LIGASE/RNA 17-DEC-02 1J1U TITLE CRYSTAL STRUCTURE OF ARCHAEAL TYROSYL-TRNA SYNTHETASE COMPLEXED WITH TITLE 2 TRNA(TYR) AND L-TYROSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA(TYR); COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TYROSYL-TRNA SYNTHETASE; COMPND 7 CHAIN: A; COMPND 8 EC: 6.1.1.1; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS IN METHANOCOCCUS JANNASCHII.; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 6 ORGANISM_TAXID: 2190; SOURCE 7 GENE: TYRS; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS AMINOACYL-TRNA SYNTHETASE, LIGASE, TRNA, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL GENOMICS, LIGASE- KEYWDS 3 RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.KOBAYASHI,O.NUREKI,R.ISHITANI,M.TUKALO,S.CUSACK,K.SAKAMOTO, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 27-DEC-23 1J1U 1 REMARK LINK REVDAT 2 24-FEB-09 1J1U 1 VERSN REVDAT 1 03-JUN-03 1J1U 0 JRNL AUTH T.KOBAYASHI,O.NUREKI,R.ISHITANI,A.YAREMCHUK,M.TUKALO, JRNL AUTH 2 S.CUSACK,K.SAKAMOTO,S.YOKOYAMA JRNL TITL STRUCTURAL BASIS FOR ORTHOGONAL TRNA SPECIFICITIES OF JRNL TITL 2 TYROSYL-TRNA SYNTHETASES FOR GENETIC CODE EXPANSION JRNL REF NAT.STRUCT.BIOL. V. 10 425 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 12754495 JRNL DOI 10.1038/NSB934 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1657649.240 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 49545 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) : 0.188 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4982 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7049 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 807 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2414 REMARK 3 NUCLEIC ACID ATOMS : 1578 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 364 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.86000 REMARK 3 B22 (A**2) : 3.86000 REMARK 3 B33 (A**2) : -7.72000 REMARK 3 B12 (A**2) : 3.02000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.22 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 BOND ANGLES (DEGREES) : 2.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.950 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) : 4.480 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.070 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.270 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.220 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 62.71 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE BOND DISTANCE BETWEEN SD AND CE IN REMARK 3 MET A 134 IS SLIGHTLY LONG. REMARK 4 REMARK 4 1J1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1000005524. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-02; 13-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL41XU; BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9132; 0.9793 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS; MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49557 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : 0.07100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.9000 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) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28200 REMARK 200 R SYM FOR SHELL (I) : 0.28200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1,6-HEXANEDIOL, AMMONIUM CHLORIDE, REMARK 280 MAGNESIUM CHLORIDE, ZINC ACETATE, SODIUM ACETATE, PH 4.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.02500 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.05000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 104.05000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.02500 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS: Y,X,-Z+1 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 156.07500 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 730 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 745 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 C B 575 REMARK 465 C B 576 REMARK 465 A B 577 REMARK 465 GLY A 203 REMARK 465 LYS A 204 REMARK 465 MET A 205 REMARK 465 SER A 206 REMARK 465 SER A 207 REMARK 465 SER A 208 REMARK 465 LYS A 209 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 NH1 ARG A 129 O HOH A 716 1.87 REMARK 500 O HOH A 504 O HOH A 706 1.91 REMARK 500 O HOH A 704 O HOH A 738 1.91 REMARK 500 O HOH A 528 O HOH A 732 1.97 REMARK 500 O HOH A 724 O HOH A 728 1.99 REMARK 500 O HOH A 724 O HOH A 729 2.00 REMARK 500 O HOH A 507 O HOH A 706 2.00 REMARK 500 O HOH A 519 O HOH A 713 2.00 REMARK 500 O HOH A 542 O HOH A 721 2.06 REMARK 500 O3' A B 574 O HOH B 282 2.13 REMARK 500 O HOH A 553 O HOH A 704 2.17 REMARK 500 O HOH A 740 O HOH A 742 2.18 REMARK 500 OP1 G B 564 O HOH B 38 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 B 553 O5' G B 553 C5' -0.087 REMARK 500 C B 562 N1 C B 562 C2 -0.072 REMARK 500 TYR A 72 CE2 TYR A 72 CD2 0.111 REMARK 500 GLU A 135 CG GLU A 135 CD 0.121 REMARK 500 LYS A 145 CD LYS A 145 CE 0.155 REMARK 500 VAL A 166 CB VAL A 166 CG2 0.149 REMARK 500 GLU A 237 CG GLU A 237 CD 0.094 REMARK 500 GLU A 293 CG GLU A 293 CD 0.097 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 B 519 C4' - C3' - O3' ANGL. DEV. = -12.7 DEGREES REMARK 500 U B 534 N1 - C1' - C2' ANGL. DEV. = 9.8 DEGREES REMARK 500 G B 547 N9 - C1' - C2' ANGL. DEV. = 8.4 DEGREES REMARK 500 U B 548 O3' - P - OP1 ANGL. DEV. = 6.9 DEGREES REMARK 500 G B 550 O3' - P - OP1 ANGL. DEV. = 7.7 DEGREES REMARK 500 G B 553 C5' - C4' - C3' ANGL. DEV. = -11.8 DEGREES REMARK 500 G B 572 O3' - P - OP2 ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG A 181 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 VAL A 188 CB - CA - C ANGL. DEV. = -14.7 DEGREES REMARK 500 VAL A 188 CG1 - CB - CG2 ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 257 NE - CZ - NH2 ANGL. DEV. = -3.8 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 2 112.88 94.53 REMARK 500 HIS A 42 -168.81 -115.72 REMARK 500 ASN A 211 13.08 -65.21 REMARK 500 CYS A 231 79.61 -163.50 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 C B 501 0.07 SIDE CHAIN REMARK 500 G B 504 0.06 SIDE CHAIN REMARK 500 U B 518 0.10 SIDE CHAIN REMARK 500 G B 520 0.07 SIDE CHAIN REMARK 500 U B 534 0.21 SIDE CHAIN REMARK 500 A B 539 0.05 SIDE CHAIN REMARK 500 C B 542 0.07 SIDE CHAIN REMARK 500 U B 546 0.12 SIDE CHAIN REMARK 500 ARG A 129 0.12 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 B1503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 18 O REMARK 620 2 HOH B 77 O 167.8 REMARK 620 3 HOH B 278 O 90.2 86.3 REMARK 620 4 HOH B 359 O 88.4 103.9 106.5 REMARK 620 5 HOH B 360 O 83.5 84.6 87.6 163.8 REMARK 620 6 HOH B 361 O 78.4 103.7 167.5 78.6 86.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 60 O REMARK 620 2 HOH B 350 O 94.2 REMARK 620 3 A B 509 OP1 81.5 105.1 REMARK 620 4 G B 510 OP2 72.2 153.8 95.1 REMARK 620 5 U B 548 OP1 159.9 89.7 116.5 96.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 61 O REMARK 620 2 HOH B 288 O 86.9 REMARK 620 3 HOH B 289 O 82.7 169.3 REMARK 620 4 HOH B 290 O 89.7 83.4 94.7 REMARK 620 5 HOH B 291 O 92.3 87.7 94.5 170.8 REMARK 620 6 HOH B 292 O 166.4 85.0 104.9 78.5 98.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 160 NE2 REMARK 620 2 HOH A 722 O 112.0 REMARK 620 3 HOH A 723 O 108.4 123.5 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 MG B 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYR A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MY_001000009.1 RELATED DB: TARGETDB DBREF 1J1U A 1 306 UNP Q57834 SYY_METJA 1 306 DBREF 1J1U B 501 577 PDB 1J1U 1J1U 501 577 SEQRES 1 B 77 C C G G C G G U A G U U C SEQRES 2 B 77 A G C C U G G U A G A A C SEQRES 3 B 77 G G C G G A C U G U A G A SEQRES 4 B 77 U C C G C A U G U C G C U SEQRES 5 B 77 G G U U C A A A U C C G G SEQRES 6 B 77 C C C G C C G G A C C A SEQRES 1 A 306 MET ASP GLU PHE GLU MET ILE LYS ARG ASN THR SER GLU SEQRES 2 A 306 ILE ILE SER GLU GLU GLU LEU ARG GLU VAL LEU LYS LYS SEQRES 3 A 306 ASP GLU LYS SER ALA TYR ILE GLY PHE GLU PRO SER GLY SEQRES 4 A 306 LYS ILE HIS LEU GLY HIS TYR LEU GLN ILE LYS LYS MET SEQRES 5 A 306 ILE ASP LEU GLN ASN ALA GLY PHE ASP ILE ILE ILE LEU SEQRES 6 A 306 LEU ALA ASP LEU HIS ALA TYR LEU ASN GLN LYS GLY GLU SEQRES 7 A 306 LEU ASP GLU ILE ARG LYS ILE GLY ASP TYR ASN LYS LYS SEQRES 8 A 306 VAL PHE GLU ALA MET GLY LEU LYS ALA LYS TYR VAL TYR SEQRES 9 A 306 GLY SER GLU PHE GLN LEU ASP LYS ASP TYR THR LEU ASN SEQRES 10 A 306 VAL TYR ARG LEU ALA LEU LYS THR THR LEU LYS ARG ALA SEQRES 11 A 306 ARG ARG SER MET GLU LEU ILE ALA ARG GLU ASP GLU ASN SEQRES 12 A 306 PRO LYS VAL ALA GLU VAL ILE TYR PRO ILE MET GLN VAL SEQRES 13 A 306 ASN ASP ILE HIS TYR LEU GLY VAL ASP VAL ALA VAL GLY SEQRES 14 A 306 GLY MET GLU GLN ARG LYS ILE HIS MET LEU ALA ARG GLU SEQRES 15 A 306 LEU LEU PRO LYS LYS VAL VAL CYS ILE HIS ASN PRO VAL SEQRES 16 A 306 LEU THR GLY LEU ASP GLY GLU GLY LYS MET SER SER SER SEQRES 17 A 306 LYS GLY ASN PHE ILE ALA VAL ASP ASP SER PRO GLU GLU SEQRES 18 A 306 ILE ARG ALA LYS ILE LYS LYS ALA TYR CYS PRO ALA GLY SEQRES 19 A 306 VAL VAL GLU GLY ASN PRO ILE MET GLU ILE ALA LYS TYR SEQRES 20 A 306 PHE LEU GLU TYR PRO LEU THR ILE LYS ARG PRO GLU LYS SEQRES 21 A 306 PHE GLY GLY ASP LEU THR VAL ASN SER TYR GLU GLU LEU SEQRES 22 A 306 GLU SER LEU PHE LYS ASN LYS GLU LEU HIS PRO MET ASP SEQRES 23 A 306 LEU LYS ASN ALA VAL ALA GLU GLU LEU ILE LYS ILE LEU SEQRES 24 A 306 GLU PRO ILE ARG LYS ARG LEU HET MG B1501 1 HET MG B1502 1 HET MG B1503 1 HET MG A 503 1 HET TYR A 401 13 HETNAM MG MAGNESIUM ION HETNAM TYR TYROSINE FORMUL 3 MG 4(MG 2+) FORMUL 7 TYR C9 H11 N O3 FORMUL 8 HOH *364(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 THR A 125 1 15 HELIX 8 8 THR A 126 MET A 134 1 9 HELIX 9 9 VAL A 146 GLY A 163 1 18 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 PHE A 248 1 10 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 ARG A 305 1 23 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 LYS A 29 PHE A 35 1 N TYR A 32 O VAL A 168 SHEET 5 A 6 PHE A 60 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 O HOH B 18 MG MG B1503 1555 1555 2.24 LINK O HOH B 60 MG MG B1501 1555 1555 2.40 LINK O HOH B 61 MG MG B1502 1555 1555 2.05 LINK O HOH B 77 MG MG B1503 1555 1555 2.31 LINK O HOH B 278 MG MG B1503 1555 1555 2.05 LINK O HOH B 288 MG MG B1502 1555 1555 2.11 LINK O HOH B 289 MG MG B1502 1555 1555 2.15 LINK O HOH B 290 MG MG B1502 1555 1555 2.35 LINK O HOH B 291 MG MG B1502 1555 1555 2.21 LINK O HOH B 292 MG MG B1502 1555 1555 2.15 LINK O HOH B 350 MG MG B1501 1555 1555 2.19 LINK O HOH B 359 MG MG B1503 1555 1555 2.20 LINK O HOH B 360 MG MG B1503 1555 1555 2.40 LINK O HOH B 361 MG MG B1503 1555 1555 2.59 LINK OP1 A B 509 MG MG B1501 1555 1555 2.08 LINK OP2 G B 510 MG MG B1501 1555 1555 2.24 LINK OP1 U B 548 MG MG B1501 1555 1555 2.41 LINK NE2 HIS A 160 MG MG A 503 1555 1555 2.17 LINK MG MG A 503 O HOH A 722 1555 1555 2.34 LINK MG MG A 503 O HOH A 723 1555 1555 2.09 CISPEP 1 ILE A 15 SER A 16 0 -0.20 CISPEP 2 TYR A 251 PRO A 252 0 -0.25 SITE 1 AC1 5 HOH B 60 HOH B 350 A B 509 G B 510 SITE 2 AC1 5 U B 548 SITE 1 AC2 6 HOH B 61 HOH B 288 HOH B 289 HOH B 290 SITE 2 AC2 6 HOH B 291 HOH B 292 SITE 1 AC3 3 HIS A 160 HOH A 722 HOH A 723 SITE 1 AC4 6 HOH B 18 HOH B 77 HOH B 278 HOH B 359 SITE 2 AC4 6 HOH B 360 HOH B 361 SITE 1 AC5 12 TYR A 32 GLY A 34 GLU A 36 LEU A 65 SITE 2 AC5 12 ALA A 67 HIS A 70 TYR A 151 GLN A 155 SITE 3 AC5 12 ASP A 158 GLN A 173 HOH A 599 HOH A 705 CRYST1 86.805 86.805 156.075 90.00 90.00 120.00 P 31 2 1 6 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 0.011520 0.006651 0.000000 0.00000 SCALE2 0.000000 0.013302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006407 0.00000