HEADER LIGASE 12-FEB-05 1WYD TITLE CRYSTAL STRUCTURE OF ASPARTYL-TRNA SYNTHETASE FROM SULFOLOBUS TOKODAII COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL ASPARTYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ASPARTYL-TRNA SYNTHETASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS TOKODAII; SOURCE 3 ORGANISM_TAXID: 273063; SOURCE 4 STRAIN: 7; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS ASPARTYL-TRNA SYNTHETASE, ARCHAEA, SULFOLOBUS TOKODAII, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MAEDA,M.T.HOSSAIN,S.UBUKATA,K.SUZUKI,T.SEKIGUCHI,A.TAKENAKA REVDAT 6 13-MAR-24 1WYD 1 REMARK REVDAT 5 13-JUL-11 1WYD 1 VERSN REVDAT 4 24-FEB-09 1WYD 1 VERSN REVDAT 3 02-OCT-07 1WYD 1 JRNL REVDAT 2 25-SEP-07 1WYD 1 JRNL REVDAT 1 04-JUL-06 1WYD 0 JRNL AUTH Y.SATO,Y.MAEDA,S.SHIMIZU,M.T.HOSSAIN,S.UBUKATA,K.SUZUKI, JRNL AUTH 2 T.SEKIGUCHI,A.TAKENAKA JRNL TITL STRUCTURE OF THE NONDISCRIMINATING ASPARTYL-TRNA SYNTHETASE JRNL TITL 2 FROM THE CRENARCHAEON SULFOLOBUS TOKODAII STRAIN 7 REVEALS JRNL TITL 3 THE RECOGNITION MECHANISM FOR TWO DIFFERENT TRNA ANTICODONS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 63 1042 2007 JRNL REFN ISSN 0907-4449 JRNL PMID 17881821 JRNL DOI 10.1107/S0907444907038292 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 48969 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 + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5476 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3496 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 406 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6781 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.08000 REMARK 3 B22 (A**2) : -2.96000 REMARK 3 B33 (A**2) : -7.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.326 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.195 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.260 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6960 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9409 ; 1.558 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 854 ; 6.273 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1048 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5172 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3311 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 400 ; 0.166 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 27 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.197 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4274 ; 0.899 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6877 ; 1.658 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2686 ; 2.364 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2532 ; 3.847 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000024149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54405 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CHLORIDE, 0.1M SODIUM REMARK 280 HEPES, 1.6M AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 58.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 69.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 58.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 69.62500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -105.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 ASN A 337 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 GLU A 13 CG CD OE1 OE2 REMARK 470 ASN A 53 CG OD1 ND2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 ARG A 80 CG CD NE CZ NH1 NH2 REMARK 470 SER A 107 OG REMARK 470 LYS A 109 CG CD CE NZ REMARK 470 VAL A 110 CG1 CG2 REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 ASP A 215 CG OD1 OD2 REMARK 470 LYS A 272 CG CD CE NZ REMARK 470 LYS A 295 CG CD CE NZ REMARK 470 GLU A 311 CG CD OE1 OE2 REMARK 470 LYS A 313 CG CD CE NZ REMARK 470 GLU A 368 CG CD OE1 OE2 REMARK 470 LYS A 371 CG CD CE NZ REMARK 470 LYS A 373 CG CD CE NZ REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 GLU A 378 CG CD OE1 OE2 REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 ARG B 80 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 109 CG CD CE NZ REMARK 470 LYS B 111 CG CD CE NZ REMARK 470 ASP B 215 CG OD1 OD2 REMARK 470 GLU B 270 CG CD OE1 OE2 REMARK 470 LYS B 272 CG CD CE NZ REMARK 470 LYS B 295 CG CD CE NZ REMARK 470 LYS B 313 CG CD CE NZ REMARK 470 SER B 335 OG REMARK 470 GLU B 336 CG CD OE1 OE2 REMARK 470 PRO B 338 CG CD REMARK 470 GLU B 339 CG CD OE1 OE2 REMARK 470 GLU B 364 CG CD OE1 OE2 REMARK 470 LYS B 376 CG CD CE NZ REMARK 470 PRO B 377 CG CD REMARK 470 GLU B 378 CG CD OE1 OE2 REMARK 470 LYS B 425 CG CD CE NZ 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 ASP A 41 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 227 CB - CG - OD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 LEU A 241 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 ASP A 321 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 388 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 MET A 405 CG - SD - CE ANGL. DEV. = -10.6 DEGREES REMARK 500 ASP B 9 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 41 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP B 113 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 PRO B 338 N - CA - CB ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP B 345 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 PRO B 377 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP B 388 CB - CG - OD2 ANGL. DEV. = 6.6 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 GLU A 13 17.97 -65.49 REMARK 500 GLU A 66 -2.38 73.18 REMARK 500 ASP A 78 -34.88 -144.11 REMARK 500 LYS A 79 0.58 57.39 REMARK 500 GLN A 189 -84.12 -6.46 REMARK 500 GLU A 200 -45.31 56.80 REMARK 500 GLU A 213 56.47 -97.00 REMARK 500 HIS A 219 54.81 -146.88 REMARK 500 ASN A 293 56.50 -102.84 REMARK 500 LYS A 313 22.90 47.59 REMARK 500 LYS A 349 -91.03 77.22 REMARK 500 SER A 357 165.76 179.65 REMARK 500 GLU B 13 17.65 -62.78 REMARK 500 VAL B 25 97.97 -63.37 REMARK 500 GLU B 66 -2.24 76.24 REMARK 500 ASP B 78 -45.21 -152.20 REMARK 500 LYS B 79 -35.26 78.21 REMARK 500 ARG B 83 18.19 52.19 REMARK 500 LYS B 109 150.73 78.13 REMARK 500 VAL B 110 101.26 -54.46 REMARK 500 ALA B 112 156.15 68.45 REMARK 500 GLN B 189 -71.62 -19.02 REMARK 500 VAL B 198 -52.67 -122.45 REMARK 500 GLU B 200 -50.54 67.50 REMARK 500 HIS B 219 51.49 -141.13 REMARK 500 ASP B 234 -168.41 -114.55 REMARK 500 PHE B 296 130.82 -38.43 REMARK 500 ASN B 337 109.26 -164.35 REMARK 500 LYS B 349 -91.44 52.26 REMARK 500 HIS B 361 -1.03 -144.75 REMARK 500 LYS B 372 -6.38 -58.30 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 EPE A 1003 REMARK 610 EPE B 1004 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 431 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE B 1004 DBREF 1WYD A 1 429 UNP Q976I3 SYD_SULTO 1 429 DBREF 1WYD B 1 429 UNP Q976I3 SYD_SULTO 1 429 SEQRES 1 A 429 MET TYR ARG SER HIS PHE ILE ALA ASP VAL THR PRO GLU SEQRES 2 A 429 TYR ASP GLY LYS GLU VAL ILE TRP ALA GLY TRP VAL HIS SEQRES 3 A 429 LEU LEU ARG ASP LEU GLY GLY LYS LYS PHE ILE ILE LEU SEQRES 4 A 429 ARG ASP LYS THR GLY LEU GLY GLN VAL VAL VAL ASP LYS SEQRES 5 A 429 ASN SER SER ALA PHE GLY ILE SER GLN GLU LEU THR GLN SEQRES 6 A 429 GLU SER VAL ILE GLN VAL ARG GLY ILE VAL LYS ALA ASP SEQRES 7 A 429 LYS ARG ALA PRO ARG GLY ILE GLU LEU HIS ALA GLU GLU SEQRES 8 A 429 ILE THR LEU LEU SER LYS ALA LYS ALA PRO LEU PRO LEU SEQRES 9 A 429 ASP VAL SER GLY LYS VAL LYS ALA ASP ILE ASP THR ARG SEQRES 10 A 429 LEU ARG GLU ARG VAL LEU ASP LEU ARG ARG GLN GLU MET SEQRES 11 A 429 GLN ALA VAL ILE LYS ILE GLN SER LEU ALA LEU LYS ALA SEQRES 12 A 429 PHE ARG GLU THR LEU TYR LYS GLU GLY PHE ILE GLU ILE SEQRES 13 A 429 PHE THR PRO LYS ILE ILE ALA SER ALA THR GLU GLY GLY SEQRES 14 A 429 ALA GLN LEU PHE PRO VAL ILE TYR PHE GLY LYS GLU ALA SEQRES 15 A 429 PHE LEU ALA GLN SER PRO GLN LEU TYR LYS GLU LEU MET SEQRES 16 A 429 ALA GLY VAL VAL GLU ARG VAL PHE GLU VAL ALA PRO ALA SEQRES 17 A 429 TRP ARG ALA GLU GLU SER ASP THR PRO PHE HIS LEU ALA SEQRES 18 A 429 GLU PHE ILE SER MET ASP VAL GLU MET ALA PHE ALA ASP SEQRES 19 A 429 TYR ASN ASP VAL MET GLN LEU LEU GLU LYS ILE LEU HIS SEQRES 20 A 429 ASN ILE VAL LYS THR ILE LYS GLU GLU GLY LYS GLU GLU SEQRES 21 A 429 LEU LYS ILE LEU ASN TYR GLU PRO PRO GLU VAL LYS ILE SEQRES 22 A 429 PRO ILE LYS ARG LEU LYS TYR THR GLU ALA ILE GLU ILE SEQRES 23 A 429 LEU ARG SER LYS GLY TYR ASN ILE LYS PHE GLY ASP ASP SEQRES 24 A 429 ILE GLY THR PRO GLU LEU ARG ILE LEU ASN GLU GLU LEU SEQRES 25 A 429 LYS GLU ASP LEU TYR PHE ILE VAL ASP TRP PRO SER ASP SEQRES 26 A 429 ALA ARG PRO PHE TYR THR LYS SER LYS SER GLU ASN PRO SEQRES 27 A 429 GLU LEU SER GLU SER PHE ASP LEU ILE TYR LYS PHE LEU SEQRES 28 A 429 GLU ILE VAL SER GLY SER THR ARG ASN HIS LYS ARG GLU SEQRES 29 A 429 VAL LEU GLU GLU ALA LEU LYS LYS LYS GLY LEU LYS PRO SEQRES 30 A 429 GLU SER PHE GLU PHE PHE LEU LYS TRP PHE ASP TYR GLY SEQRES 31 A 429 MET PRO PRO HIS ALA GLY PHE GLY MET GLY LEU ALA ARG SEQRES 32 A 429 LEU MET VAL MET LEU THR GLY ILE GLN SER VAL LYS GLU SEQRES 33 A 429 ILE VAL PRO PHE PRO ARG ASP LYS LYS ARG LEU THR PRO SEQRES 1 B 429 MET TYR ARG SER HIS PHE ILE ALA ASP VAL THR PRO GLU SEQRES 2 B 429 TYR ASP GLY LYS GLU VAL ILE TRP ALA GLY TRP VAL HIS SEQRES 3 B 429 LEU LEU ARG ASP LEU GLY GLY LYS LYS PHE ILE ILE LEU SEQRES 4 B 429 ARG ASP LYS THR GLY LEU GLY GLN VAL VAL VAL ASP LYS SEQRES 5 B 429 ASN SER SER ALA PHE GLY ILE SER GLN GLU LEU THR GLN SEQRES 6 B 429 GLU SER VAL ILE GLN VAL ARG GLY ILE VAL LYS ALA ASP SEQRES 7 B 429 LYS ARG ALA PRO ARG GLY ILE GLU LEU HIS ALA GLU GLU SEQRES 8 B 429 ILE THR LEU LEU SER LYS ALA LYS ALA PRO LEU PRO LEU SEQRES 9 B 429 ASP VAL SER GLY LYS VAL LYS ALA ASP ILE ASP THR ARG SEQRES 10 B 429 LEU ARG GLU ARG VAL LEU ASP LEU ARG ARG GLN GLU MET SEQRES 11 B 429 GLN ALA VAL ILE LYS ILE GLN SER LEU ALA LEU LYS ALA SEQRES 12 B 429 PHE ARG GLU THR LEU TYR LYS GLU GLY PHE ILE GLU ILE SEQRES 13 B 429 PHE THR PRO LYS ILE ILE ALA SER ALA THR GLU GLY GLY SEQRES 14 B 429 ALA GLN LEU PHE PRO VAL ILE TYR PHE GLY LYS GLU ALA SEQRES 15 B 429 PHE LEU ALA GLN SER PRO GLN LEU TYR LYS GLU LEU MET SEQRES 16 B 429 ALA GLY VAL VAL GLU ARG VAL PHE GLU VAL ALA PRO ALA SEQRES 17 B 429 TRP ARG ALA GLU GLU SER ASP THR PRO PHE HIS LEU ALA SEQRES 18 B 429 GLU PHE ILE SER MET ASP VAL GLU MET ALA PHE ALA ASP SEQRES 19 B 429 TYR ASN ASP VAL MET GLN LEU LEU GLU LYS ILE LEU HIS SEQRES 20 B 429 ASN ILE VAL LYS THR ILE LYS GLU GLU GLY LYS GLU GLU SEQRES 21 B 429 LEU LYS ILE LEU ASN TYR GLU PRO PRO GLU VAL LYS ILE SEQRES 22 B 429 PRO ILE LYS ARG LEU LYS TYR THR GLU ALA ILE GLU ILE SEQRES 23 B 429 LEU ARG SER LYS GLY TYR ASN ILE LYS PHE GLY ASP ASP SEQRES 24 B 429 ILE GLY THR PRO GLU LEU ARG ILE LEU ASN GLU GLU LEU SEQRES 25 B 429 LYS GLU ASP LEU TYR PHE ILE VAL ASP TRP PRO SER ASP SEQRES 26 B 429 ALA ARG PRO PHE TYR THR LYS SER LYS SER GLU ASN PRO SEQRES 27 B 429 GLU LEU SER GLU SER PHE ASP LEU ILE TYR LYS PHE LEU SEQRES 28 B 429 GLU ILE VAL SER GLY SER THR ARG ASN HIS LYS ARG GLU SEQRES 29 B 429 VAL LEU GLU GLU ALA LEU LYS LYS LYS GLY LEU LYS PRO SEQRES 30 B 429 GLU SER PHE GLU PHE PHE LEU LYS TRP PHE ASP TYR GLY SEQRES 31 B 429 MET PRO PRO HIS ALA GLY PHE GLY MET GLY LEU ALA ARG SEQRES 32 B 429 LEU MET VAL MET LEU THR GLY ILE GLN SER VAL LYS GLU SEQRES 33 B 429 ILE VAL PRO PHE PRO ARG ASP LYS LYS ARG LEU THR PRO HET CL A 431 1 HET SO4 A1001 5 HET EPE A1003 12 HET CL B 430 1 HET SO4 B1002 5 HET EPE B1004 12 HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 CL 2(CL 1-) FORMUL 4 SO4 2(O4 S 2-) FORMUL 5 EPE 2(C8 H18 N2 O4 S) FORMUL 9 HOH *276(H2 O) HELIX 1 1 THR A 11 ASP A 15 5 5 HELIX 2 2 ALA A 56 GLN A 61 1 6 HELIX 3 3 ALA A 81 ARG A 83 5 3 HELIX 4 4 ASP A 113 GLU A 120 1 8 HELIX 5 5 GLU A 120 ARG A 126 1 7 HELIX 6 6 ARG A 127 GLU A 151 1 25 HELIX 7 7 PRO A 188 GLU A 200 1 13 HELIX 8 8 ASP A 234 GLY A 257 1 24 HELIX 9 9 GLY A 257 ASN A 265 1 9 HELIX 10 10 TYR A 280 LYS A 290 1 11 HELIX 11 11 GLY A 301 LYS A 313 1 13 HELIX 12 12 PRO A 323 ARG A 327 5 5 HELIX 13 13 LYS A 362 LYS A 373 1 12 HELIX 14 14 LYS A 376 SER A 379 5 4 HELIX 15 15 PHE A 380 LYS A 385 1 6 HELIX 16 16 TRP A 386 TYR A 389 5 4 HELIX 17 17 LEU A 401 GLY A 410 1 10 HELIX 18 18 SER A 413 ILE A 417 5 5 HELIX 19 19 PHE B 6 VAL B 10 5 5 HELIX 20 20 THR B 11 ASP B 15 5 5 HELIX 21 21 ALA B 56 GLN B 61 1 6 HELIX 22 22 ALA B 81 ARG B 83 5 3 HELIX 23 23 ASP B 113 ARG B 119 1 7 HELIX 24 24 GLU B 120 ARG B 126 1 7 HELIX 25 25 ARG B 127 GLU B 151 1 25 HELIX 26 26 PRO B 188 GLU B 200 1 13 HELIX 27 27 ASP B 234 GLY B 257 1 24 HELIX 28 28 GLY B 257 ASN B 265 1 9 HELIX 29 29 TYR B 280 LYS B 290 1 11 HELIX 30 30 GLY B 301 LYS B 313 1 13 HELIX 31 31 PRO B 323 ARG B 327 5 5 HELIX 32 32 LYS B 362 LYS B 372 1 11 HELIX 33 33 LYS B 376 SER B 379 5 4 HELIX 34 34 PHE B 380 LYS B 385 1 6 HELIX 35 35 TRP B 386 TYR B 389 5 4 HELIX 36 36 LEU B 401 GLY B 410 1 10 SHEET 1 A 6 GLU A 18 LEU A 31 0 SHEET 2 A 6 LYS A 34 ASP A 41 -1 O PHE A 36 N ARG A 29 SHEET 3 A 6 GLY A 44 VAL A 50 -1 O VAL A 48 N ILE A 37 SHEET 4 A 6 ILE A 85 SER A 96 1 O LEU A 87 N GLN A 47 SHEET 5 A 6 VAL A 68 ALA A 77 -1 N GLN A 70 O THR A 93 SHEET 6 A 6 GLU A 18 LEU A 31 -1 N GLY A 23 O ILE A 69 SHEET 1 B 8 ILE A 154 GLU A 155 0 SHEET 2 B 8 ARG A 201 TRP A 209 1 O ARG A 201 N ILE A 154 SHEET 3 B 8 GLU A 222 ALA A 231 -1 O ASP A 227 N GLU A 204 SHEET 4 B 8 HIS A 394 GLY A 400 -1 O MET A 399 N MET A 226 SHEET 5 B 8 LEU A 351 THR A 358 -1 N SER A 355 O GLY A 398 SHEET 6 B 8 SER A 343 TYR A 348 -1 N LEU A 346 O ILE A 353 SHEET 7 B 8 LEU A 316 VAL A 320 -1 N TYR A 317 O ILE A 347 SHEET 8 B 8 LYS A 276 LYS A 279 1 N LEU A 278 O PHE A 318 SHEET 1 C 3 ILE A 161 ILE A 162 0 SHEET 2 C 3 LYS A 180 LEU A 184 -1 O PHE A 183 N ILE A 162 SHEET 3 C 3 PRO A 174 TYR A 177 -1 N VAL A 175 O ALA A 182 SHEET 1 D 6 GLU B 18 LEU B 31 0 SHEET 2 D 6 LYS B 34 ASP B 41 -1 O PHE B 36 N ARG B 29 SHEET 3 D 6 GLY B 44 VAL B 50 -1 O VAL B 48 N ILE B 37 SHEET 4 D 6 ILE B 85 SER B 96 1 O ALA B 89 N VAL B 49 SHEET 5 D 6 VAL B 68 ALA B 77 -1 N VAL B 68 O SER B 96 SHEET 6 D 6 GLU B 18 LEU B 31 -1 N TRP B 21 O VAL B 71 SHEET 1 E 8 ILE B 154 GLU B 155 0 SHEET 2 E 8 ARG B 201 TRP B 209 1 O ARG B 201 N ILE B 154 SHEET 3 E 8 GLU B 222 ALA B 231 -1 O ASP B 227 N GLU B 204 SHEET 4 E 8 HIS B 394 GLY B 400 -1 O ALA B 395 N MET B 230 SHEET 5 E 8 LEU B 351 THR B 358 -1 N SER B 355 O GLY B 398 SHEET 6 E 8 SER B 343 TYR B 348 -1 N LEU B 346 O ILE B 353 SHEET 7 E 8 LEU B 316 VAL B 320 -1 N ILE B 319 O ASP B 345 SHEET 8 E 8 LYS B 276 LYS B 279 1 N LYS B 276 O PHE B 318 SHEET 1 F 3 ILE B 161 ILE B 162 0 SHEET 2 F 3 LYS B 180 LEU B 184 -1 O PHE B 183 N ILE B 162 SHEET 3 F 3 PRO B 174 TYR B 177 -1 N VAL B 175 O ALA B 182 CISPEP 1 ALA A 100 PRO A 101 0 -5.90 CISPEP 2 ILE A 273 PRO A 274 0 5.80 CISPEP 3 THR A 428 PRO A 429 0 5.19 CISPEP 4 ALA B 100 PRO B 101 0 -2.10 CISPEP 5 ILE B 273 PRO B 274 0 6.66 CISPEP 6 THR B 428 PRO B 429 0 7.08 SITE 1 AC1 4 THR A 166 GLU A 167 GLN A 186 HOH A1038 SITE 1 AC2 5 PRO A 217 PHE A 218 SER A 413 VAL A 414 SITE 2 AC2 5 LYS A 415 SITE 1 AC3 3 THR B 166 GLU B 167 GLN B 186 SITE 1 AC4 7 THR B 216 PRO B 217 PHE B 218 SER B 413 SITE 2 AC4 7 VAL B 414 LYS B 415 HOH B1152 SITE 1 AC5 8 PHE A 218 HIS A 219 LEU A 220 PHE A 223 SITE 2 AC5 8 ARG A 403 VAL A 414 HOH A1027 HOH A1057 SITE 1 AC6 6 PHE B 218 HIS B 219 LEU B 220 PHE B 223 SITE 2 AC6 6 ARG B 403 HOH B1046 CRYST1 116.300 139.250 75.300 90.00 90.00 90.00 P 21 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 0.008598 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013280 0.00000