PDB Short entry for 1O9B HEADER OXIDOREDUCTASE 12-DEC-02 1O9B TITLE QUINATE/SHIKIMATE DEHYDROGENASE YDIB COMPLEXED WITH NADH COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL SHIKIMATE 5-DEHYDROGENASE-LIKE PROTEIN YDIB; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.25; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: MC1061 P3; SOURCE 5 ATCC: 47035; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DL41(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T1; SOURCE 11 OTHER_DETAILS: GST-TAG, SELEMETHIONYL PROTEIN KEYWDS OXIDOREDUCTASE, QUINATE, SHIKIMATE, NAD, MONTREAL-KINGSTON BACTERIAL KEYWDS 2 STRUCTURAL GENOMICS INITIATIVE, BSGI, STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR G.MICHEL,M.CYGLER REVDAT 4 30-OCT-13 1O9B 1 COMPND SOURCE KEYWDS JRNL REVDAT 4 2 REMARK VERSN HET HETNAM REVDAT 4 3 HETSYN FORMUL SITE HETATM REVDAT 4 4 MASTER REVDAT 3 24-FEB-09 1O9B 1 VERSN REVDAT 2 22-MAY-03 1O9B 1 JRNL REVDAT 1 01-FEB-03 1O9B 0 JRNL AUTH G.MICHEL,A.W.ROSZAK,V.SAUVE,J.MCLEAN,A.MATTE,J.R.COGGINS, JRNL AUTH 2 M.CYGLER,A.J.LAPTHORN JRNL TITL STRUCTURES OF SHIKIMATE DEHYDROGENASE AROE AND ITS PARALOG JRNL TITL 2 YDIB: A COMMON STRUCTURAL FRAMEWORK FOR DIFFERENT JRNL TITL 3 ACTIVITIES JRNL REF J.BIOL.CHEM. V. 278 19463 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12637497 JRNL DOI 10.1074/JBC.M300794200 REMARK 2 REMARK 2 RESOLUTION. 2.5 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1887922.36 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20116 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) : 0.226 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.8 REMARK 3 FREE R VALUE TEST SET COUNT : 972 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3139 REMARK 3 BIN R VALUE (WORKING SET) : 0.267 REMARK 3 BIN FREE R VALUE : 0.372 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.9 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 162 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4114 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 273 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.1 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.85 REMARK 3 B22 (A**2) : -1.85 REMARK 3 B33 (A**2) : 3.70 REMARK 3 B12 (A**2) : 4.10 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.30 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) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.50 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.6 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.7 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.92 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 : 0.313499 REMARK 3 BSOL : 57.8041 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NAD.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NAD.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1O9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-02. REMARK 100 THE PDBE ID CODE IS EBI-11853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97161 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38407 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.880 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 7.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.305 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: KH2PO4, NAH2PO4, HEPES REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 13.33700 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 26.67400 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.33700 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 26.67400 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 MSE A 1 REMARK 465 ASP A 2 REMARK 465 VAL A 3 REMARK 465 THR A 4 REMARK 465 ALA A 5 REMARK 465 LYS A 6 REMARK 465 ALA A 288 REMARK 465 MSE B 1 REMARK 465 ASP B 2 REMARK 465 VAL B 3 REMARK 465 THR B 4 REMARK 465 ALA B 5 REMARK 465 LYS B 6 REMARK 465 ALA B 288 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 GLY A 287 CA C O REMARK 470 GLY B 287 CA C O REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; REMARK 480 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 480 I=INSERTION CODE): REMARK 480 M RES CSSEQI ATOMS REMARK 480 TYR A 15 CE1 CE2 CZ OH REMARK 480 HIS A 19 CG ND1 CD2 CE1 NE2 REMARK 480 LYS A 57 CE NZ REMARK 480 LYS A 60 CE NZ REMARK 480 LYS A 86 CE NZ REMARK 480 ALA A 132 CB REMARK 480 ARG A 157 CA CB CG CD NE REMARK 480 ASP A 158 CG OD1 OD2 REMARK 480 GLN A 169 CG CD OE1 NE2 REMARK 480 VAL A 181 CG1 CG2 REMARK 480 ASP A 183 CG OD1 OD2 REMARK 480 LEU A 184 CG CD1 CD2 REMARK 480 ALA A 185 CB REMARK 480 GLN A 187 CG CD OE1 NE2 REMARK 480 PRO A 210 C CB CG REMARK 480 LEU A 211 CD1 CD2 REMARK 480 GLU A 212 CG CD OE1 OE2 REMARK 480 ASN A 235 CB CG OD1 ND2 REMARK 480 GLN A 247 CG CD OE1 NE2 REMARK 480 TYR B 15 OH REMARK 480 HIS B 19 CG ND1 CD2 CE1 NE2 REMARK 480 LYS B 209 CD CE NZ REMARK 480 GLU B 214 CG CD OE1 OE2 REMARK 480 GLN B 247 CD OE1 NE2 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 LYS A 209 O - C - N ANGL. DEV. = -20.2 DEGREES 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 TYR A 15 114.32 -161.93 REMARK 500 LYS A 32 46.85 -71.87 REMARK 500 ALA A 33 1.64 -169.71 REMARK 500 ALA A 90 145.36 -178.49 REMARK 500 ALA A 132 13.82 -157.42 REMARK 500 GLN A 187 -3.44 -41.23 REMARK 500 GLN A 188 -63.28 -109.77 REMARK 500 LEU A 211 41.31 -62.48 REMARK 500 ASN A 213 46.40 -144.43 REMARK 500 PRO A 236 -156.02 -77.78 REMARK 500 GLN A 246 -19.25 -48.55 REMARK 500 GLN A 247 -79.36 -66.35 REMARK 500 ALA A 248 -0.54 -52.54 REMARK 500 GLN A 282 -71.27 -54.37 REMARK 500 TYR B 15 116.67 -164.31 REMARK 500 ILE B 17 -25.90 -142.54 REMARK 500 ARG B 18 -16.84 -48.52 REMARK 500 PRO B 36 49.23 -76.33 REMARK 500 ALA B 90 138.01 -170.11 REMARK 500 ASP B 97 74.13 -107.29 REMARK 500 ALA B 132 27.96 -157.86 REMARK 500 GLU B 146 36.33 -92.58 REMARK 500 ASN B 155 126.47 -172.45 REMARK 500 ASP B 158 -159.96 -132.66 REMARK 500 GLU B 192 -78.50 -71.02 REMARK 500 ALA B 193 -36.03 -35.92 REMARK 500 LEU B 211 50.83 -107.63 REMARK 500 SER B 221 34.54 -93.22 REMARK 500 PRO B 225 -86.98 -58.34 REMARK 500 ASN B 235 111.01 174.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 209 -35.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI B 301 DBREF 1O9B A 1 288 UNP P28244 YDIB_ECOLI 1 288 DBREF 1O9B B 1 288 UNP P28244 YDIB_ECOLI 1 288 SEQRES 1 A 288 MSE ASP VAL THR ALA LYS TYR GLU LEU ILE GLY LEU MSE SEQRES 2 A 288 ALA TYR PRO ILE ARG HIS SER LEU SER PRO GLU MSE GLN SEQRES 3 A 288 ASN LYS ALA LEU GLU LYS ALA GLY LEU PRO PHE THR TYR SEQRES 4 A 288 MSE ALA PHE GLU VAL ASP ASN ASP SER PHE PRO GLY ALA SEQRES 5 A 288 ILE GLU GLY LEU LYS ALA LEU LYS MSE ARG GLY THR GLY SEQRES 6 A 288 VAL SER MSE PRO ASN LYS GLN LEU ALA CYS GLU TYR VAL SEQRES 7 A 288 ASP GLU LEU THR PRO ALA ALA LYS LEU VAL GLY ALA ILE SEQRES 8 A 288 ASN THR ILE VAL ASN ASP ASP GLY TYR LEU ARG GLY TYR SEQRES 9 A 288 ASN THR ASP GLY THR GLY HIS ILE ARG ALA ILE LYS GLU SEQRES 10 A 288 SER GLY PHE ASP ILE LYS GLY LYS THR MSE VAL LEU LEU SEQRES 11 A 288 GLY ALA GLY GLY ALA SER THR ALA ILE GLY ALA GLN GLY SEQRES 12 A 288 ALA ILE GLU GLY LEU LYS GLU ILE LYS LEU PHE ASN ARG SEQRES 13 A 288 ARG ASP GLU PHE PHE ASP LYS ALA LEU ALA PHE ALA GLN SEQRES 14 A 288 ARG VAL ASN GLU ASN THR ASP CYS VAL VAL THR VAL THR SEQRES 15 A 288 ASP LEU ALA ASP GLN GLN ALA PHE ALA GLU ALA LEU ALA SEQRES 16 A 288 SER ALA ASP ILE LEU THR ASN GLY THR LYS VAL GLY MSE SEQRES 17 A 288 LYS PRO LEU GLU ASN GLU SER LEU VAL ASN ASP ILE SER SEQRES 18 A 288 LEU LEU HIS PRO GLY LEU LEU VAL THR GLU CYS VAL TYR SEQRES 19 A 288 ASN PRO HIS MSE THR LYS LEU LEU GLN GLN ALA GLN GLN SEQRES 20 A 288 ALA GLY CYS LYS THR ILE ASP GLY TYR GLY MSE LEU LEU SEQRES 21 A 288 TRP GLN GLY ALA GLU GLN PHE THR LEU TRP THR GLY LYS SEQRES 22 A 288 ASP PHE PRO LEU GLU TYR VAL LYS GLN VAL MSE GLY PHE SEQRES 23 A 288 GLY ALA SEQRES 1 B 288 MSE ASP VAL THR ALA LYS TYR GLU LEU ILE GLY LEU MSE SEQRES 2 B 288 ALA TYR PRO ILE ARG HIS SER LEU SER PRO GLU MSE GLN SEQRES 3 B 288 ASN LYS ALA LEU GLU LYS ALA GLY LEU PRO PHE THR TYR SEQRES 4 B 288 MSE ALA PHE GLU VAL ASP ASN ASP SER PHE PRO GLY ALA SEQRES 5 B 288 ILE GLU GLY LEU LYS ALA LEU LYS MSE ARG GLY THR GLY SEQRES 6 B 288 VAL SER MSE PRO ASN LYS GLN LEU ALA CYS GLU TYR VAL SEQRES 7 B 288 ASP GLU LEU THR PRO ALA ALA LYS LEU VAL GLY ALA ILE SEQRES 8 B 288 ASN THR ILE VAL ASN ASP ASP GLY TYR LEU ARG GLY TYR SEQRES 9 B 288 ASN THR ASP GLY THR GLY HIS ILE ARG ALA ILE LYS GLU SEQRES 10 B 288 SER GLY PHE ASP ILE LYS GLY LYS THR MSE VAL LEU LEU SEQRES 11 B 288 GLY ALA GLY GLY ALA SER THR ALA ILE GLY ALA GLN GLY SEQRES 12 B 288 ALA ILE GLU GLY LEU LYS GLU ILE LYS LEU PHE ASN ARG SEQRES 13 B 288 ARG ASP GLU PHE PHE ASP LYS ALA LEU ALA PHE ALA GLN SEQRES 14 B 288 ARG VAL ASN GLU ASN THR ASP CYS VAL VAL THR VAL THR SEQRES 15 B 288 ASP LEU ALA ASP GLN GLN ALA PHE ALA GLU ALA LEU ALA SEQRES 16 B 288 SER ALA ASP ILE LEU THR ASN GLY THR LYS VAL GLY MSE SEQRES 17 B 288 LYS PRO LEU GLU ASN GLU SER LEU VAL ASN ASP ILE SER SEQRES 18 B 288 LEU LEU HIS PRO GLY LEU LEU VAL THR GLU CYS VAL TYR SEQRES 19 B 288 ASN PRO HIS MSE THR LYS LEU LEU GLN GLN ALA GLN GLN SEQRES 20 B 288 ALA GLY CYS LYS THR ILE ASP GLY TYR GLY MSE LEU LEU SEQRES 21 B 288 TRP GLN GLY ALA GLU GLN PHE THR LEU TRP THR GLY LYS SEQRES 22 B 288 ASP PHE PRO LEU GLU TYR VAL LYS GLN VAL MSE GLY PHE SEQRES 23 B 288 GLY ALA MODRES 1O9B MSE A 13 MET SELENOMETHIONINE MODRES 1O9B MSE A 25 MET SELENOMETHIONINE MODRES 1O9B MSE A 40 MET SELENOMETHIONINE MODRES 1O9B MSE A 61 MET SELENOMETHIONINE MODRES 1O9B MSE A 68 MET SELENOMETHIONINE MODRES 1O9B MSE A 127 MET SELENOMETHIONINE MODRES 1O9B MSE A 208 MET SELENOMETHIONINE MODRES 1O9B MSE A 238 MET SELENOMETHIONINE MODRES 1O9B MSE A 258 MET SELENOMETHIONINE MODRES 1O9B MSE A 284 MET SELENOMETHIONINE MODRES 1O9B MSE B 13 MET SELENOMETHIONINE MODRES 1O9B MSE B 25 MET SELENOMETHIONINE MODRES 1O9B MSE B 40 MET SELENOMETHIONINE MODRES 1O9B MSE B 61 MET SELENOMETHIONINE MODRES 1O9B MSE B 68 MET SELENOMETHIONINE MODRES 1O9B MSE B 127 MET SELENOMETHIONINE MODRES 1O9B MSE B 208 MET SELENOMETHIONINE MODRES 1O9B MSE B 238 MET SELENOMETHIONINE MODRES 1O9B MSE B 258 MET SELENOMETHIONINE MODRES 1O9B MSE B 284 MET SELENOMETHIONINE HET MSE A 13 8 HET MSE A 25 8 HET MSE A 40 8 HET MSE A 61 8 HET MSE A 68 8 HET MSE A 127 8 HET MSE A 208 8 HET MSE A 238 8 HET MSE A 258 8 HET MSE A 284 8 HET MSE B 13 8 HET MSE B 25 8 HET MSE B 40 8 HET MSE B 61 8 HET MSE B 68 8 HET MSE B 127 8 HET MSE B 208 8 HET MSE B 238 8 HET MSE B 258 8 HET MSE B 284 8 HET PO4 A 302 5 HET PO4 A 303 5 HET PO4 A 304 5 HET PO4 B 302 5 HET PO4 B 303 5 HET NAI A 301 44 HET NAI B 301 44 HETNAM MSE SELENOMETHIONINE HETNAM PO4 PHOSPHATE ION HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETSYN NAI NADH FORMUL 1 MSE 20(C5 H11 N O2 SE) FORMUL 3 PO4 5(O4 P 3-) FORMUL 8 NAI 2(C21 H29 N7 O14 P2) FORMUL 10 HOH *154(H2 O) HELIX 1 1 LEU A 21 LYS A 32 1 12 HELIX 2 2 SER A 48 LEU A 59 1 12 HELIX 3 3 GLN A 72 VAL A 78 5 7 HELIX 4 4 THR A 82 GLY A 89 1 8 HELIX 5 5 ASN A 105 GLU A 117 1 13 HELIX 6 6 GLY A 133 GLU A 146 1 14 HELIX 7 7 PHE A 160 THR A 175 1 16 HELIX 8 8 PHE A 190 ALA A 197 1 8 HELIX 9 9 THR A 239 GLY A 249 1 11 HELIX 10 10 ASP A 254 GLY A 272 1 19 HELIX 11 11 PRO A 276 MSE A 284 1 9 HELIX 12 12 LEU B 21 ALA B 33 1 13 HELIX 13 13 SER B 48 LEU B 59 1 12 HELIX 14 14 ASN B 70 CYS B 75 1 6 HELIX 15 15 THR B 82 GLY B 89 1 8 HELIX 16 16 ASN B 105 GLU B 117 1 13 HELIX 17 17 GLY B 133 GLU B 146 1 14 HELIX 18 18 GLU B 159 THR B 175 1 17 HELIX 19 19 ASP B 186 SER B 196 1 11 HELIX 20 20 THR B 239 GLN B 246 1 8 HELIX 21 21 ASP B 254 GLY B 272 1 19 HELIX 22 22 PRO B 276 MSE B 284 1 9 SHEET 1 AA 5 PHE A 37 GLU A 43 0 SHEET 2 AA 5 GLU A 8 ALA A 14 1 O GLU A 8 N THR A 38 SHEET 3 AA 5 GLY A 63 VAL A 66 1 O GLY A 63 N GLY A 11 SHEET 4 AA 5 THR A 93 ASP A 97 -1 O ILE A 94 N THR A 64 SHEET 5 AA 5 TYR A 100 TYR A 104 -1 O TYR A 100 N ASP A 97 SHEET 1 AB 6 VAL A 178 THR A 182 0 SHEET 2 AB 6 GLU A 150 PHE A 154 1 O ILE A 151 N THR A 180 SHEET 3 AB 6 THR A 126 LEU A 130 1 O MSE A 127 N LYS A 152 SHEET 4 AB 6 ILE A 199 ASN A 202 1 O ILE A 199 N VAL A 128 SHEET 5 AB 6 LEU A 228 GLU A 231 1 O LEU A 228 N LEU A 200 SHEET 6 AB 6 LYS A 251 ILE A 253 1 O LYS A 251 N VAL A 229 SHEET 1 BA 6 PHE B 37 GLU B 43 0 SHEET 2 BA 6 GLU B 8 ALA B 14 1 O GLU B 8 N THR B 38 SHEET 3 BA 6 GLY B 63 VAL B 66 1 O GLY B 63 N GLY B 11 SHEET 4 BA 6 THR B 93 ASP B 97 -1 O ILE B 94 N THR B 64 SHEET 5 BA 6 TYR B 100 TYR B 104 -1 O TYR B 100 N ASP B 97 SHEET 6 BA 6 GLU B 80 LEU B 81 1 O GLU B 80 N GLY B 103 SHEET 1 BB 6 VAL B 178 THR B 182 0 SHEET 2 BB 6 GLU B 150 PHE B 154 1 O ILE B 151 N THR B 180 SHEET 3 BB 6 THR B 126 LEU B 130 1 O MSE B 127 N LYS B 152 SHEET 4 BB 6 ILE B 199 ASN B 202 1 O ILE B 199 N VAL B 128 SHEET 5 BB 6 LEU B 228 GLU B 231 1 O LEU B 228 N LEU B 200 SHEET 6 BB 6 LYS B 251 ILE B 253 1 O LYS B 251 N VAL B 229 LINK C LEU A 12 N MSE A 13 1555 1555 1.33 LINK C MSE A 13 N ALA A 14 1555 1555 1.33 LINK C GLU A 24 N MSE A 25 1555 1555 1.33 LINK C MSE A 25 N GLN A 26 1555 1555 1.33 LINK C TYR A 39 N MSE A 40 1555 1555 1.32 LINK C MSE A 40 N ALA A 41 1555 1555 1.32 LINK C LYS A 60 N MSE A 61 1555 1555 1.33 LINK C MSE A 61 N ARG A 62 1555 1555 1.33 LINK C SER A 67 N MSE A 68 1555 1555 1.32 LINK C MSE A 68 N PRO A 69 1555 1555 1.34 LINK C THR A 126 N MSE A 127 1555 1555 1.33 LINK C MSE A 127 N VAL A 128 1555 1555 1.32 LINK C GLY A 207 N MSE A 208 1555 1555 1.33 LINK C MSE A 208 N LYS A 209 1555 1555 1.35 LINK C HIS A 237 N MSE A 238 1555 1555 1.33 LINK C MSE A 238 N THR A 239 1555 1555 1.33 LINK C GLY A 257 N MSE A 258 1555 1555 1.33 LINK C MSE A 258 N LEU A 259 1555 1555 1.33 LINK C VAL A 283 N MSE A 284 1555 1555 1.33 LINK C MSE A 284 N GLY A 285 1555 1555 1.33 LINK C LEU B 12 N MSE B 13 1555 1555 1.33 LINK C MSE B 13 N ALA B 14 1555 1555 1.33 LINK C GLU B 24 N MSE B 25 1555 1555 1.33 LINK C MSE B 25 N GLN B 26 1555 1555 1.33 LINK C TYR B 39 N MSE B 40 1555 1555 1.32 LINK C MSE B 40 N ALA B 41 1555 1555 1.32 LINK C LYS B 60 N MSE B 61 1555 1555 1.33 LINK C MSE B 61 N ARG B 62 1555 1555 1.33 LINK C SER B 67 N MSE B 68 1555 1555 1.33 LINK C MSE B 68 N PRO B 69 1555 1555 1.34 LINK C THR B 126 N MSE B 127 1555 1555 1.33 LINK C MSE B 127 N VAL B 128 1555 1555 1.33 LINK C GLY B 207 N MSE B 208 1555 1555 1.34 LINK C MSE B 208 N LYS B 209 1555 1555 1.33 LINK C HIS B 237 N MSE B 238 1555 1555 1.33 LINK C MSE B 238 N THR B 239 1555 1555 1.33 LINK C GLY B 257 N MSE B 258 1555 1555 1.33 LINK C MSE B 258 N LEU B 259 1555 1555 1.33 LINK C VAL B 283 N MSE B 284 1555 1555 1.33 LINK C MSE B 284 N GLY B 285 1555 1555 1.33 CISPEP 1 TYR A 15 PRO A 16 0 -5.23 CISPEP 2 MSE A 68 PRO A 69 0 1.65 CISPEP 3 LYS A 209 PRO A 210 0 -0.08 CISPEP 4 ASN A 235 PRO A 236 0 -0.09 CISPEP 5 TYR B 15 PRO B 16 0 0.14 CISPEP 6 MSE B 68 PRO B 69 0 0.84 CISPEP 7 LYS B 209 PRO B 210 0 0.14 CISPEP 8 ASN B 235 PRO B 236 0 0.38 SITE 1 AC1 5 SER A 67 LYS A 71 ASP A 107 NAI A 301 SITE 2 AC1 5 HOH A2088 SITE 1 AC2 5 MSE A 68 PRO A 69 ASN A 70 LYS A 71 SITE 2 AC2 5 GLN A 72 SITE 1 AC3 6 LYS A 32 TYR A 100 LYS A 149 GLU A 150 SITE 2 AC3 6 LYS A 152 SER A 196 SITE 1 AC4 5 SER B 67 LYS B 71 ASP B 107 NAI B 301 SITE 2 AC4 5 HOH B2065 SITE 1 AC5 7 MSE B 68 PRO B 69 ASN B 70 LYS B 71 SITE 2 AC5 7 GLN B 72 HOH B2062 HOH B2066 SITE 1 AC6 19 ALA A 132 GLY A 133 GLY A 134 ALA A 135 SITE 2 AC6 19 ASN A 155 ARG A 156 PHE A 160 GLY A 203 SITE 3 AC6 19 THR A 204 LYS A 205 VAL A 206 MSE A 208 SITE 4 AC6 19 CYS A 232 TYR A 234 GLY A 255 MSE A 258 SITE 5 AC6 19 LEU A 259 PO4 A 302 HOH A2058 SITE 1 AC7 25 ASP B 107 ALA B 132 GLY B 133 GLY B 134 SITE 2 AC7 25 ALA B 135 ASN B 155 ARG B 156 ASP B 158 SITE 3 AC7 25 PHE B 160 GLY B 203 THR B 204 LYS B 205 SITE 4 AC7 25 VAL B 206 MSE B 208 CYS B 232 VAL B 233 SITE 5 AC7 25 TYR B 234 GLY B 255 MSE B 258 LEU B 259 SITE 6 AC7 25 PO4 B 302 HOH B2044 HOH B2062 HOH B2063 SITE 7 AC7 25 HOH B2064 CRYST1 157.874 157.874 40.011 90.00 90.00 120.00 P 64 12 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 0.006334 0.003657 0.000000 0.00000 SCALE2 0.000000 0.007314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024993 0.00000 MTRIX1 1 -0.982750 -0.065340 -0.173020 238.74544 1 MTRIX2 1 0.107990 -0.962200 -0.250020 81.28804 1 MTRIX3 1 -0.150150 -0.264390 0.952660 30.46164 1