HEADER OXIDOREDUCTASE 02-DEC-05 2D8A TITLE CRYSTAL STRUCTURE OF PH0655 FROM PYROCOCCUS HORIKOSHII OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE L-THREONINE 3-DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PH0655; COMPND 5 EC: 1.1.1.103; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS PYROCOCCUS HORIKOSHII OT3, STRUCTURAL GENOMICS, PH0655, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, NPPSFA, NATIONAL KEYWDS 3 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 4 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ASADA,N.KUNISHIMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 2 (RSGI) REVDAT 3 13-JUL-11 2D8A 1 VERSN REVDAT 2 24-FEB-09 2D8A 1 VERSN REVDAT 1 02-JUN-06 2D8A 0 JRNL AUTH Y.ASADA,N.KUNISHIMA JRNL TITL CRYSTAL STRUCTURE OF PH0655 FROM PYROCOCCUS HORIKOSHII OT3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.05 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 29497 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) : 0.204 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1481 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.14 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 171 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2540 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 263 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.46000 REMARK 3 B22 (A**2) : -5.60000 REMARK 3 B33 (A**2) : 1.14000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-DEC-05. REMARK 100 THE RCSB ID CODE IS RCSB025111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97924 REMARK 200 MONOCHROMATOR : BENDING MAGNET REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29497 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : 0.24400 REMARK 200 FOR SHELL : 5.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (V/V) 1,2-PROPANEDIOL, 10% (V/V) REMARK 280 GLYCEROL, IMIDAZOLE PH 8.0, 0.2M ZN(OAC)2, PH 5.9, MICROBATCH, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 42.54200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.71800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.20650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.54200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.71800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 61.20650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.54200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.71800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.20650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.54200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.71800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.20650 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: TETRAMERIC 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 -1.000000 0.000000 0.000000 85.08400 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 89.43600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 85.08400 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 89.43600 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 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 687 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 649 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 650 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 MSE A 1 REMARK 465 SER A 2 REMARK 465 ALA A 102 REMARK 465 CYS A 103 REMARK 465 ARG A 104 REMARK 465 ARG A 105 REMARK 465 GLY A 106 REMARK 465 GLN A 107 REMARK 465 TYR A 108 REMARK 465 HIS A 109 REMARK 465 VAL A 110 REMARK 465 CYS A 111 REMARK 465 GLN A 112 REMARK 465 ASN A 113 REMARK 465 LYS A 348 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 TRP A 297 NE1 TRP A 297 CE2 0.107 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 HIS A 67 -21.17 -145.07 REMARK 500 ILE A 166 -19.44 -145.72 REMARK 500 TYR A 193 130.17 -172.49 REMARK 500 LYS A 327 31.26 -91.66 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 A 673 DISTANCE = 5.13 ANGSTROMS REMARK 525 HOH A 674 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A 675 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH A 729 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH A 730 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A 733 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH A 734 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A 739 DISTANCE = 5.79 ANGSTROMS REMARK 525 HOH A 759 DISTANCE = 5.41 ANGSTROMS 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 NE2 REMARK 620 2 GLU A 68 OE1 117.4 REMARK 620 3 HOH A 762 O 110.2 108.8 REMARK 620 4 CYS A 42 SG 103.2 88.6 128.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 92 OE2 REMARK 620 2 GLU A 152 OE2 139.7 REMARK 620 3 HIS A 295 ND1 107.1 90.6 REMARK 620 4 GLU A 152 OE1 88.0 51.9 117.7 REMARK 620 5 GLU A 92 OE1 52.9 111.0 62.9 84.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 HOH A 635 O 93.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 221 OE1 REMARK 620 2 GLU A 221 OE2 59.3 REMARK 620 3 HOH A 765 O 108.5 101.5 REMARK 620 4 GLU A 127 OE2 102.7 160.3 91.5 REMARK 620 5 GLU A 127 OE1 83.8 113.1 144.5 53.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 222 OE2 REMARK 620 2 HOH A 766 O 104.9 REMARK 620 3 ASP A 326 OD2 94.0 81.6 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 ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PH0001000655.1 RELATED DB: TARGETDB DBREF 2D8A A 1 348 UNP O58389 TDH_PYRHO 1 348 SEQADV 2D8A MSE A 1 UNP O58389 MET 1 MODIFIED RESIDUE SEQADV 2D8A MSE A 5 UNP O58389 MET 5 MODIFIED RESIDUE SEQADV 2D8A MSE A 9 UNP O58389 MET 9 MODIFIED RESIDUE SEQADV 2D8A MSE A 65 UNP O58389 MET 65 MODIFIED RESIDUE SEQADV 2D8A MSE A 229 UNP O58389 MET 229 MODIFIED RESIDUE SEQADV 2D8A MSE A 335 UNP O58389 MET 335 MODIFIED RESIDUE SEQADV 2D8A MSE A 346 UNP O58389 MET 346 MODIFIED RESIDUE SEQRES 1 A 348 MSE SER GLU LYS MSE VAL ALA ILE MSE LYS THR LYS PRO SEQRES 2 A 348 GLY TYR GLY ALA GLU LEU VAL GLU VAL ASP VAL PRO LYS SEQRES 3 A 348 PRO GLY PRO GLY GLU VAL LEU ILE LYS VAL LEU ALA THR SEQRES 4 A 348 SER ILE CYS GLY THR ASP LEU HIS ILE TYR GLU TRP ASN SEQRES 5 A 348 GLU TRP ALA GLN SER ARG ILE LYS PRO PRO GLN ILE MSE SEQRES 6 A 348 GLY HIS GLU VAL ALA GLY GLU VAL VAL GLU ILE GLY PRO SEQRES 7 A 348 GLY VAL GLU GLY ILE GLU VAL GLY ASP TYR VAL SER VAL SEQRES 8 A 348 GLU THR HIS ILE VAL CYS GLY LYS CYS TYR ALA CYS ARG SEQRES 9 A 348 ARG GLY GLN TYR HIS VAL CYS GLN ASN THR LYS ILE PHE SEQRES 10 A 348 GLY VAL ASP THR ASP GLY VAL PHE ALA GLU TYR ALA VAL SEQRES 11 A 348 VAL PRO ALA GLN ASN ILE TRP LYS ASN PRO LYS SER ILE SEQRES 12 A 348 PRO PRO GLU TYR ALA THR LEU GLN GLU PRO LEU GLY ASN SEQRES 13 A 348 ALA VAL ASP THR VAL LEU ALA GLY PRO ILE SER GLY LYS SEQRES 14 A 348 SER VAL LEU ILE THR GLY ALA GLY PRO LEU GLY LEU LEU SEQRES 15 A 348 GLY ILE ALA VAL ALA LYS ALA SER GLY ALA TYR PRO VAL SEQRES 16 A 348 ILE VAL SER GLU PRO SER ASP PHE ARG ARG GLU LEU ALA SEQRES 17 A 348 LYS LYS VAL GLY ALA ASP TYR VAL ILE ASN PRO PHE GLU SEQRES 18 A 348 GLU ASP VAL VAL LYS GLU VAL MSE ASP ILE THR ASP GLY SEQRES 19 A 348 ASN GLY VAL ASP VAL PHE LEU GLU PHE SER GLY ALA PRO SEQRES 20 A 348 LYS ALA LEU GLU GLN GLY LEU GLN ALA VAL THR PRO ALA SEQRES 21 A 348 GLY ARG VAL SER LEU LEU GLY LEU TYR PRO GLY LYS VAL SEQRES 22 A 348 THR ILE ASP PHE ASN ASN LEU ILE ILE PHE LYS ALA LEU SEQRES 23 A 348 THR ILE TYR GLY ILE THR GLY ARG HIS LEU TRP GLU THR SEQRES 24 A 348 TRP TYR THR VAL SER ARG LEU LEU GLN SER GLY LYS LEU SEQRES 25 A 348 ASN LEU ASP PRO ILE ILE THR HIS LYS TYR LYS GLY PHE SEQRES 26 A 348 ASP LYS TYR GLU GLU ALA PHE GLU LEU MSE ARG ALA GLY SEQRES 27 A 348 LYS THR GLY LYS VAL VAL PHE MSE LEU LYS MODRES 2D8A MSE A 5 MET SELENOMETHIONINE MODRES 2D8A MSE A 9 MET SELENOMETHIONINE MODRES 2D8A MSE A 65 MET SELENOMETHIONINE MODRES 2D8A MSE A 229 MET SELENOMETHIONINE MODRES 2D8A MSE A 335 MET SELENOMETHIONINE MODRES 2D8A MSE A 346 MET SELENOMETHIONINE HET MSE A 5 8 HET MSE A 9 8 HET MSE A 65 8 HET MSE A 229 8 HET MSE A 335 8 HET MSE A 346 8 HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET ZN A 505 1 HET NAD A 401 44 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 ZN 5(ZN 2+) FORMUL 7 NAD C21 H27 N7 O14 P2 FORMUL 8 HOH *263(H2 O) HELIX 1 1 CYS A 42 TRP A 51 1 10 HELIX 2 2 TRP A 54 ILE A 59 1 6 HELIX 3 3 PRO A 144 THR A 149 1 6 HELIX 4 4 LEU A 150 LEU A 162 1 13 HELIX 5 5 GLY A 177 SER A 190 1 14 HELIX 6 6 SER A 201 GLY A 212 1 12 HELIX 7 7 ASP A 223 THR A 232 1 10 HELIX 8 8 ALA A 246 ALA A 256 1 11 HELIX 9 9 ASP A 276 ILE A 281 1 6 HELIX 10 10 LEU A 296 GLY A 310 1 15 HELIX 11 11 LYS A 327 ALA A 337 1 11 SHEET 1 A 3 GLU A 18 ASP A 23 0 SHEET 2 A 3 LYS A 4 LYS A 10 -1 N MSE A 9 O GLU A 18 SHEET 3 A 3 GLN A 63 ILE A 64 -1 O GLN A 63 N LYS A 10 SHEET 1 B 5 TYR A 128 PRO A 132 0 SHEET 2 B 5 GLU A 31 SER A 40 -1 N ILE A 34 O ALA A 129 SHEET 3 B 5 GLU A 68 ILE A 76 -1 O GLU A 75 N LEU A 33 SHEET 4 B 5 TYR A 88 VAL A 91 -1 O VAL A 89 N GLY A 71 SHEET 5 B 5 ILE A 136 LYS A 138 -1 O TRP A 137 N SER A 90 SHEET 1 C 4 TYR A 128 PRO A 132 0 SHEET 2 C 4 GLU A 31 SER A 40 -1 N ILE A 34 O ALA A 129 SHEET 3 C 4 LYS A 342 MSE A 346 -1 O PHE A 345 N THR A 39 SHEET 4 C 4 ILE A 318 LYS A 323 1 N TYR A 322 O MSE A 346 SHEET 1 D 2 HIS A 94 ILE A 95 0 SHEET 2 D 2 LYS A 115 ILE A 116 -1 O LYS A 115 N ILE A 95 SHEET 1 E 6 TYR A 215 ILE A 217 0 SHEET 2 E 6 VAL A 195 SER A 198 1 N VAL A 197 O ILE A 217 SHEET 3 E 6 VAL A 171 THR A 174 1 N ILE A 173 O ILE A 196 SHEET 4 E 6 VAL A 237 GLU A 242 1 O LEU A 241 N LEU A 172 SHEET 5 E 6 VAL A 257 LEU A 265 1 O THR A 258 N VAL A 237 SHEET 6 E 6 THR A 287 GLY A 290 1 O TYR A 289 N LEU A 265 LINK ZN ZN A 501 NE2 HIS A 67 1555 1555 2.22 LINK ZN ZN A 501 OE1 GLU A 68 1555 1555 2.23 LINK ZN ZN A 502 OE2 GLU A 92 1555 1555 1.92 LINK ZN ZN A 502 OE2 GLU A 152 1555 1555 2.27 LINK ZN ZN A 502 ND1 HIS A 295 1555 1555 2.03 LINK ZN ZN A 503 NE2 HIS A 94 1555 1555 2.07 LINK ZN ZN A 504 OE1 GLU A 221 1555 1555 2.15 LINK ZN ZN A 504 OE2 GLU A 221 1555 1555 2.28 LINK ZN ZN A 505 OE2 GLU A 222 1555 1555 2.00 LINK C LYS A 4 N MSE A 5 1555 1555 1.33 LINK C MSE A 5 N VAL A 6 1555 1555 1.33 LINK C ILE A 8 N MSE A 9 1555 1555 1.33 LINK C MSE A 9 N LYS A 10 1555 1555 1.33 LINK C ILE A 64 N MSE A 65 1555 1555 1.33 LINK C MSE A 65 N GLY A 66 1555 1555 1.33 LINK C VAL A 228 N MSE A 229 1555 1555 1.33 LINK C MSE A 229 N ASP A 230 1555 1555 1.33 LINK C LEU A 334 N MSE A 335 1555 1555 1.33 LINK C MSE A 335 N ARG A 336 1555 1555 1.33 LINK C PHE A 345 N MSE A 346 1555 1555 1.33 LINK C MSE A 346 N LEU A 347 1555 1555 1.33 LINK ZN ZN A 501 O HOH A 762 1555 1555 1.93 LINK ZN ZN A 502 OE1 GLU A 152 1555 1555 2.69 LINK ZN ZN A 502 OE1 GLU A 92 1555 1555 2.73 LINK ZN ZN A 503 O HOH A 635 1555 1555 2.39 LINK ZN ZN A 504 O HOH A 765 1555 1555 2.48 LINK ZN ZN A 505 O HOH A 766 1555 1555 1.97 LINK ZN ZN A 504 OE2 GLU A 127 1555 7555 2.40 LINK ZN ZN A 504 OE1 GLU A 127 1555 7555 2.53 LINK ZN ZN A 505 OD2 ASP A 326 1555 7555 2.20 LINK SG CYS A 42 ZN ZN A 501 1555 1555 2.86 CISPEP 1 PRO A 61 PRO A 62 0 -0.18 CISPEP 2 TYR A 193 PRO A 194 0 -0.35 SITE 1 AC1 4 CYS A 42 HIS A 67 GLU A 68 HOH A 762 SITE 1 AC2 3 GLU A 92 GLU A 152 HIS A 295 SITE 1 AC3 5 HIS A 94 HIS A 295 HOH A 634 HOH A 635 SITE 2 AC3 5 HOH A 763 SITE 1 AC4 4 GLU A 127 GLU A 221 HOH A 764 HOH A 765 SITE 1 AC5 3 GLU A 222 ASP A 326 HOH A 766 SITE 1 AC6 23 GLY A 175 GLY A 177 PRO A 178 LEU A 179 SITE 2 AC6 23 SER A 198 GLU A 199 PRO A 200 ARG A 204 SITE 3 AC6 23 PHE A 243 SER A 244 ALA A 246 LEU A 266 SITE 4 AC6 23 GLY A 267 LEU A 268 ILE A 282 ILE A 291 SITE 5 AC6 23 THR A 292 HOH A 509 HOH A 516 HOH A 580 SITE 6 AC6 23 HOH A 592 HOH A 732 HOH A 747 CRYST1 85.084 89.436 122.413 90.00 90.00 90.00 I 2 2 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 0.011753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008169 0.00000