10 20 30 40 50 60 70 80 1WD7 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 12-MAY-04 1WD7
TITLE CRYSTAL STRUCTURE OF UROPORPHYRINOGEN III SYNTHASE FROM AN TITLE 2 EXTREMELY THERMOPHILIC BACTERIUM THERMUS THERMOPHILUS HB8 TITLE 3 (WILD TYPE, NATIVE, FORM-2 CRYSTAL)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: UROPORPHYRINOGEN III SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.2.1.75; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET
KEYWDS UROPORPHYRINOGEN, PORPHYRIN, HEME, CONGENITAL KEYWDS 2 ERYTHROPOIETIC PORPHYRIA, STRUCTURAL GENOMICS, RIKEN KEYWDS 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR E.MIZOHATA,T.MATSUURA,H.SAKAI,K.MURAYAMA,T.TERADA, AUTHOR 2 M.SHIROUZU,S.KURAMITSU,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 3 GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 3 24-FEB-09 1WD7 1 VERSN REVDAT 2 17-MAY-05 1WD7 1 AUTHOR KEYWDS REMARK REVDAT 1 12-NOV-04 1WD7 0
JRNL AUTH E.MIZOHATA,T.MATSUURA,H.SAKAI,K.MURAYAMA,T.TERADA, JRNL AUTH 2 M.SHIROUZU,S.KURAMITSU,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF UROPORPHYRINOGEN III SYNTHASE JRNL TITL 2 FROM AN EXTREMELY THERMOPHILIC BACTERIUM THERMUS JRNL TITL 3 THERMOPHILUS HB8 (WILD TYPE, NATIVE, FORM-2 JRNL TITL 4 CRYSTAL) JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 994489.340 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.7 REMARK 3 NUMBER OF REFLECTIONS : 53494 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) : 0.224 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2710 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8261 REMARK 3 BIN R VALUE (WORKING SET) : 0.3190 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 466 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3894 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 463 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.59000 REMARK 3 B22 (A**2) : -3.81000 REMARK 3 B33 (A**2) : 4.40000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.90000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.23 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.80 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.38 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 50.50 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 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : RUB.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : RUB.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1WD7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAY-04. REMARK 100 THE RCSB ID CODE IS RCSB023451.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1WCW REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 42.43750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 BIOLOGICAL ASSEMBLY IS BELIEVED TO BE A MONOMER.
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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 ARG A 3 REMARK 465 LEU A 4 REMARK 465 GLU A 5 REMARK 465 GLU A 6 REMARK 465 ASP A 7 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 ARG B 3 REMARK 465 LEU B 4 REMARK 465 GLU B 5 REMARK 465 GLU B 6
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 NE2 GLN B 129 NH1 ARG B 153 1.57 REMARK 500 NZ LYS A 121 O HOH A 494 1.75 REMARK 500 NH2 ARG B 244 OG SER B 247 1.79 REMARK 500 O ALA B 261 O HOH B 398 1.96 REMARK 500 NH1 ARG B 244 OG SER B 247 2.01 REMARK 500 NH2 ARG A 174 O HOH A 267 2.01 REMARK 500 O HOH A 365 O HOH A 367 2.03 REMARK 500 NH1 ARG A 153 O HOH A 439 2.03 REMARK 500 O ARG B 254 N GLN B 257 2.04 REMARK 500 CD2 LEU A 173 O HOH A 476 2.04 REMARK 500 O HOH B 463 O HOH B 479 2.07 REMARK 500 O HOH B 343 O HOH B 477 2.07 REMARK 500 NH2 ARG B 164 O HOH B 336 2.07 REMARK 500 O HOH A 320 O HOH A 395 2.10 REMARK 500 CZ ARG B 244 OG SER B 247 2.11 REMARK 500 O HOH A 452 O HOH A 485 2.14 REMARK 500 CD2 LEU B 25 O HOH B 475 2.15 REMARK 500 O GLN A 129 O HOH A 454 2.15 REMARK 500 NE2 GLN B 129 CZ ARG B 153 2.17 REMARK 500 OE2 GLU A 177 O HOH A 374 2.18 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 OE1 GLU A 20 CZ ARG B 254 2645 1.72 REMARK 500 NZ LYS B 106 O HOH A 282 1455 1.82 REMARK 500 NZ LYS A 258 O HOH A 464 1655 1.91 REMARK 500 CE LYS A 28 O HOH A 457 1655 1.95 REMARK 500 NZ LYS A 28 O HOH A 457 1655 1.96 REMARK 500 OE1 GLU A 20 NH1 ARG B 254 2645 1.98 REMARK 500 NH2 ARG A 254 O HOH A 475 1655 1.99 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 PHE B 252 CB PHE B 252 CG -0.149 REMARK 500 GLN B 257 CA GLN B 257 C 0.167 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 103 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 164 NE - CZ - NH1 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A 164 NE - CZ - NH2 ANGL. DEV. = 6.3 DEGREES REMARK 500 LYS A 235 CD - CE - NZ ANGL. DEV. = 28.4 DEGREES REMARK 500 LEU B 16 CA - CB - CG ANGL. DEV. = 20.7 DEGREES REMARK 500 ARG B 17 N - CA - C ANGL. DEV. = 17.6 DEGREES REMARK 500 LYS B 43 N - CA - CB ANGL. DEV. = -13.0 DEGREES REMARK 500 THR B 214 N - CA - CB ANGL. DEV. = -22.3 DEGREES REMARK 500 LEU B 256 N - CA - C ANGL. DEV. = -17.5 DEGREES REMARK 500 GLN B 257 CB - CA - C ANGL. DEV. = 18.6 DEGREES REMARK 500 GLN B 257 C - N - CA ANGL. DEV. = -21.3 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 17 -83.21 -41.82 REMARK 500 ARG A 18 64.78 -108.02 REMARK 500 THR A 214 -65.81 -138.24 REMARK 500 THR B 214 -78.09 -140.93 REMARK 500 GLU B 243 32.36 72.73 REMARK 500 GLU B 259 66.26 -107.18 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 103 0.12 SIDE_CHAIN REMARK 500 ARG A 153 0.15 SIDE_CHAIN REMARK 500 ARG A 164 0.26 SIDE_CHAIN 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 B 316 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 319 DISTANCE = 5.62 ANGSTROMS REMARK 525 HOH B 339 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 365 DISTANCE = 10.56 ANGSTROMS REMARK 525 HOH A 366 DISTANCE = 9.90 ANGSTROMS REMARK 525 HOH A 367 DISTANCE = 8.86 ANGSTROMS REMARK 525 HOH A 372 DISTANCE = 5.08 ANGSTROMS REMARK 525 HOH A 382 DISTANCE = 8.22 ANGSTROMS REMARK 525 HOH A 383 DISTANCE = 11.38 ANGSTROMS REMARK 525 HOH B 383 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH B 385 DISTANCE = 7.29 ANGSTROMS REMARK 525 HOH A 388 DISTANCE = 7.77 ANGSTROMS REMARK 525 HOH A 393 DISTANCE = 7.90 ANGSTROMS REMARK 525 HOH B 407 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH A 410 DISTANCE = 7.67 ANGSTROMS REMARK 525 HOH A 414 DISTANCE = 5.19 ANGSTROMS REMARK 525 HOH A 423 DISTANCE = 8.92 ANGSTROMS REMARK 525 HOH A 424 DISTANCE = 12.07 ANGSTROMS REMARK 525 HOH A 445 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH B 452 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH B 459 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH A 464 DISTANCE = 7.51 ANGSTROMS REMARK 525 HOH A 468 DISTANCE = 5.44 ANGSTROMS REMARK 525 HOH A 480 DISTANCE = 5.55 ANGSTROMS REMARK 525 HOH A 482 DISTANCE = 9.40 ANGSTROMS REMARK 525 HOH B 483 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH B 488 DISTANCE = 6.38 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WCW RELATED DB: PDB REMARK 900 WILD-TYPE, NATIVE, FORM-1 CRYSTAL REMARK 900 RELATED ID: 1WCX RELATED DB: PDB REMARK 900 L75M/I193M/L248M, SEMET DERIVATIVE, FORM-1 CRYSTAL REMARK 900 RELATED ID: TTK003001434.1 RELATED DB: TARGETDB
DBREF 1WD7 A 10 261 UNP Q5SKH2 Q5SKH2_THET8 2 253 DBREF 1WD7 B 10 261 UNP Q5SKH2 Q5SKH2_THET8 2 253
SEQRES 1 A 261 MET ARG ARG LEU GLU GLU ASP ALA VAL ARG VAL ALA TYR SEQRES 2 A 261 ALA GLY LEU ARG ARG LYS GLU ALA PHE LYS ALA LEU ALA SEQRES 3 A 261 GLU LYS LEU GLY PHE THR PRO LEU LEU PHE PRO VAL GLN SEQRES 4 A 261 ALA THR GLU LYS VAL PRO VAL PRO GLU TYR ARG ASP GLN SEQRES 5 A 261 VAL ARG ALA LEU ALA GLN GLY VAL ASP LEU PHE LEU ALA SEQRES 6 A 261 THR THR GLY VAL GLY VAL ARG ASP LEU LEU GLU ALA GLY SEQRES 7 A 261 LYS ALA LEU GLY LEU ASP LEU GLU GLY PRO LEU ALA LYS SEQRES 8 A 261 ALA PHE ARG LEU ALA ARG GLY ALA LYS ALA ALA ARG ALA SEQRES 9 A 261 LEU LYS GLU ALA GLY LEU PRO PRO HIS ALA VAL GLY ASP SEQRES 10 A 261 GLY THR SER LYS SER LEU LEU PRO LEU LEU PRO GLN GLY SEQRES 11 A 261 ARG GLY VAL ALA ALA LEU GLN LEU TYR GLY LYS PRO LEU SEQRES 12 A 261 PRO LEU LEU GLU ASN ALA LEU ALA GLU ARG GLY TYR ARG SEQRES 13 A 261 VAL LEU PRO LEU MET PRO TYR ARG HIS LEU PRO ASP PRO SEQRES 14 A 261 GLU GLY ILE LEU ARG LEU GLU GLU ALA LEU LEU ARG GLY SEQRES 15 A 261 GLU VAL ASP ALA LEU ALA PHE VAL ALA ALA ILE GLN VAL SEQRES 16 A 261 GLU PHE LEU PHE GLU GLY ALA LYS ASP PRO LYS ALA LEU SEQRES 17 A 261 ARG GLU ALA LEU ASN THR ARG VAL LYS ALA LEU ALA VAL SEQRES 18 A 261 GLY ARG VAL THR ALA ASP ALA LEU ARG GLU TRP GLY VAL SEQRES 19 A 261 LYS PRO PHE TYR VAL ASP GLU THR GLU ARG LEU GLY SER SEQRES 20 A 261 LEU LEU GLN GLY PHE LYS ARG ALA LEU GLN LYS GLU VAL SEQRES 21 A 261 ALA SEQRES 1 B 261 MET ARG ARG LEU GLU GLU ASP ALA VAL ARG VAL ALA TYR SEQRES 2 B 261 ALA GLY LEU ARG ARG LYS GLU ALA PHE LYS ALA LEU ALA SEQRES 3 B 261 GLU LYS LEU GLY PHE THR PRO LEU LEU PHE PRO VAL GLN SEQRES 4 B 261 ALA THR GLU LYS VAL PRO VAL PRO GLU TYR ARG ASP GLN SEQRES 5 B 261 VAL ARG ALA LEU ALA GLN GLY VAL ASP LEU PHE LEU ALA SEQRES 6 B 261 THR THR GLY VAL GLY VAL ARG ASP LEU LEU GLU ALA GLY SEQRES 7 B 261 LYS ALA LEU GLY LEU ASP LEU GLU GLY PRO LEU ALA LYS SEQRES 8 B 261 ALA PHE ARG LEU ALA ARG GLY ALA LYS ALA ALA ARG ALA SEQRES 9 B 261 LEU LYS GLU ALA GLY LEU PRO PRO HIS ALA VAL GLY ASP SEQRES 10 B 261 GLY THR SER LYS SER LEU LEU PRO LEU LEU PRO GLN GLY SEQRES 11 B 261 ARG GLY VAL ALA ALA LEU GLN LEU TYR GLY LYS PRO LEU SEQRES 12 B 261 PRO LEU LEU GLU ASN ALA LEU ALA GLU ARG GLY TYR ARG SEQRES 13 B 261 VAL LEU PRO LEU MET PRO TYR ARG HIS LEU PRO ASP PRO SEQRES 14 B 261 GLU GLY ILE LEU ARG LEU GLU GLU ALA LEU LEU ARG GLY SEQRES 15 B 261 GLU VAL ASP ALA LEU ALA PHE VAL ALA ALA ILE GLN VAL SEQRES 16 B 261 GLU PHE LEU PHE GLU GLY ALA LYS ASP PRO LYS ALA LEU SEQRES 17 B 261 ARG GLU ALA LEU ASN THR ARG VAL LYS ALA LEU ALA VAL SEQRES 18 B 261 GLY ARG VAL THR ALA ASP ALA LEU ARG GLU TRP GLY VAL SEQRES 19 B 261 LYS PRO PHE TYR VAL ASP GLU THR GLU ARG LEU GLY SER SEQRES 20 B 261 LEU LEU GLN GLY PHE LYS ARG ALA LEU GLN LYS GLU VAL SEQRES 21 B 261 ALA
FORMUL 3 HOH *463(H2 O)
HELIX 1 1 ARG A 18 LEU A 29 1 12 HELIX 2 2 GLU A 48 GLN A 58 1 11 HELIX 3 3 THR A 67 LEU A 81 1 15 HELIX 4 4 LEU A 85 LYS A 91 1 7 HELIX 5 5 GLY A 98 ALA A 108 1 11 HELIX 6 6 THR A 119 LEU A 127 5 9 HELIX 7 7 LEU A 143 ARG A 153 1 11 HELIX 8 8 ASP A 168 ARG A 181 1 14 HELIX 9 9 ALA A 191 ALA A 202 1 12 HELIX 10 10 ASP A 204 THR A 214 1 11 HELIX 11 11 GLY A 222 TRP A 232 1 11 HELIX 12 12 ARG A 244 ALA A 261 1 18 HELIX 13 13 ARG B 18 LEU B 29 1 12 HELIX 14 14 GLU B 48 GLN B 58 1 11 HELIX 15 15 THR B 67 LEU B 81 1 15 HELIX 16 16 LEU B 85 LYS B 91 1 7 HELIX 17 17 GLY B 98 ALA B 108 1 11 HELIX 18 18 THR B 119 LEU B 127 5 9 HELIX 19 19 LEU B 143 ARG B 153 1 11 HELIX 20 20 ASP B 168 ARG B 181 1 14 HELIX 21 21 ALA B 191 ALA B 202 1 12 HELIX 22 22 ASP B 204 LEU B 212 1 9 HELIX 23 23 GLY B 222 TRP B 232 1 11 HELIX 24 24 ARG B 244 GLU B 259 1 16
SHEET 1 A 5 THR A 32 LEU A 35 0 SHEET 2 A 5 ARG A 10 TYR A 13 1 N VAL A 11 O LEU A 34 SHEET 3 A 5 ALA A 186 PHE A 189 1 O ALA A 188 N ALA A 12 SHEET 4 A 5 LYS A 217 VAL A 221 1 O LEU A 219 N LEU A 187 SHEET 5 A 5 TYR A 238 ASP A 240 1 O ASP A 240 N ALA A 220 SHEET 1 B 2 VAL A 44 PRO A 45 0 SHEET 2 B 2 TYR A 163 ARG A 164 -1 O ARG A 164 N VAL A 44 SHEET 1 C 5 ALA A 114 VAL A 115 0 SHEET 2 C 5 PHE A 93 ALA A 96 1 N ALA A 96 O ALA A 114 SHEET 3 C 5 LEU A 62 ALA A 65 1 N PHE A 63 O LEU A 95 SHEET 4 C 5 GLY A 132 GLN A 137 1 O GLN A 137 N LEU A 64 SHEET 5 C 5 TYR A 155 LEU A 160 1 O LEU A 158 N ALA A 134 SHEET 1 D 5 THR B 32 LEU B 35 0 SHEET 2 D 5 ARG B 10 TYR B 13 1 N VAL B 11 O LEU B 34 SHEET 3 D 5 ALA B 186 PHE B 189 1 O ALA B 188 N ALA B 12 SHEET 4 D 5 LYS B 217 VAL B 221 1 O LEU B 219 N LEU B 187 SHEET 5 D 5 TYR B 238 ASP B 240 1 O ASP B 240 N ALA B 220 SHEET 1 E 2 VAL B 44 PRO B 45 0 SHEET 2 E 2 TYR B 163 ARG B 164 -1 O ARG B 164 N VAL B 44 SHEET 1 F 5 ALA B 114 VAL B 115 0 SHEET 2 F 5 PHE B 93 ALA B 96 1 N ALA B 96 O ALA B 114 SHEET 3 F 5 LEU B 62 ALA B 65 1 N PHE B 63 O PHE B 93 SHEET 4 F 5 GLY B 132 GLN B 137 1 O ALA B 135 N LEU B 64 SHEET 5 F 5 TYR B 155 LEU B 160 1 O LEU B 160 N LEU B 136
CRYST1 37.900 84.875 73.948 90.00 91.25 90.00 P 1 21 1 4
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 0.026385 0.000000 0.000578 0.00000
SCALE2 0.000000 0.011782 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013526 0.00000