HEADER OXIDOREDUCTASE 07-FEB-08 3C7D TITLE A STRUCTURAL BASIS FOR SUBSTRATE AND STEREO SELECTIVITY IN OCTOPINE TITLE 2 DEHYDROGENASE (ODH-NADH-PYRUVATE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: OCTOPINE DEHYDROGENASE; COMPND 3 CHAIN: B; COMPND 4 EC: 1.5.1.11; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PECTEN MAXIMUS; SOURCE 3 ORGANISM_COMMON: KING SCALLOP; SOURCE 4 ORGANISM_TAXID: 6579; SOURCE 5 GENE: ODH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: E.COLI ER2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PTYB1; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTYB1-ODH5HIS KEYWDS (D, L) STEREOSPECIFIC OPINE DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.H.J.SMITS,A.MUELLER,L.SCHMITT,M.K.GRIESHABER REVDAT 5 15-NOV-23 3C7D 1 REMARK ATOM REVDAT 4 30-AUG-23 3C7D 1 REMARK REVDAT 3 12-JAN-10 3C7D 1 JRNL REVDAT 2 24-FEB-09 3C7D 1 VERSN REVDAT 1 22-JUL-08 3C7D 0 JRNL AUTH S.H.SMITS,A.MUELLER,L.SCHMITT,M.K.GRIESHABER JRNL TITL A STRUCTURAL BASIS FOR SUBSTRATE SELECTIVITY AND JRNL TITL 2 STEREOSELECTIVITY IN OCTOPINE DEHYDROGENASE FROM PECTEN JRNL TITL 3 MAXIMUS. JRNL REF J.MOL.BIOL. V. 381 200 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18599075 JRNL DOI 10.1016/J.JMB.2008.06.003 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16311 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) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 859 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1151 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2991 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : 0.82000 REMARK 3 B33 (A**2) : -1.63000 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): 0.555 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.299 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.247 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.682 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.875 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3119 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4242 ; 1.035 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 393 ; 4.951 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;37.382 ;24.390 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 507 ;14.895 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;12.645 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 481 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2324 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1443 ; 0.177 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2113 ; 0.296 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 87 ; 0.113 ; 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): 43 ; 0.120 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.152 ; 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): 2011 ; 0.217 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3133 ; 0.393 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1272 ; 0.358 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1108 ; 0.599 ; 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3C7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : INTEGRATE (XDS) REMARK 200 DATA SCALING SOFTWARE : XSCALE XDS) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17525 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : 0.36100 REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3C7A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 7.0, 1.15 M NA-CITRATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 58.90000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.45000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.35000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.45000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.35000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.90000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 B 1 REMARK 465 GLU B 281 REMARK 465 TYR B 282 REMARK 465 TYR B 283 REMARK 465 HIS B 284 REMARK 465 GLU B 285 REMARK 465 ASP B 286 REMARK 465 ILE B 287 REMARK 465 GLN B 288 REMARK 465 ASP B 289 REMARK 465 ASP B 290 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 CD2 HIS B 403 OXT PYR B 406 3545 2.05 REMARK 500 CB HIS B 404 CB PYR B 406 3545 2.06 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 SER B 117 C GLN B 118 N -0.335 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 SER B 117 CA - C - N ANGL. DEV. = -24.5 DEGREES REMARK 500 SER B 117 O - C - N ANGL. DEV. = 18.8 DEGREES REMARK 500 GLN B 118 CA - C - N ANGL. DEV. = 27.3 DEGREES REMARK 500 GLN B 118 O - C - N ANGL. DEV. = -24.6 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 ALA B 36 -109.25 50.42 REMARK 500 LYS B 58 66.53 60.85 REMARK 500 THR B 61 -117.35 57.00 REMARK 500 SER B 117 -128.38 107.57 REMARK 500 GLN B 118 -139.13 30.30 REMARK 500 GLU B 152 117.28 -165.36 REMARK 500 SER B 222 54.35 -104.75 REMARK 500 PHE B 234 -88.08 -76.89 REMARK 500 TYR B 279 133.88 172.72 REMARK 500 THR B 299 34.77 -97.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN B 118 ALA B 119 -143.61 REMARK 500 VAL B 272 LYS B 273 -142.54 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 SER B 117 11.53 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 NAD B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PYR B 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C7A RELATED DB: PDB REMARK 900 RELATED ID: 3C7C RELATED DB: PDB DBREF 3C7D B 1 399 UNP Q9BHM6 Q9BHM6_PECMA 1 399 SEQADV 3C7D HIS B 400 UNP Q9BHM6 EXPRESSION TAG SEQADV 3C7D HIS B 401 UNP Q9BHM6 EXPRESSION TAG SEQADV 3C7D HIS B 402 UNP Q9BHM6 EXPRESSION TAG SEQADV 3C7D HIS B 403 UNP Q9BHM6 EXPRESSION TAG SEQADV 3C7D HIS B 404 UNP Q9BHM6 EXPRESSION TAG SEQRES 1 B 404 MET THR VAL LYS VAL CYS VAL CYS GLY GLY GLY ASN GLY SEQRES 2 B 404 ALA HIS THR LEU SER GLY LEU ALA ALA SER ARG ASP GLY SEQRES 3 B 404 VAL GLU VAL ARG VAL LEU THR LEU PHE ALA ASP GLU ALA SEQRES 4 B 404 GLU ARG TRP THR LYS ALA LEU GLY ALA ASP GLU LEU THR SEQRES 5 B 404 VAL ILE VAL ASN GLU LYS ASP GLY THR GLN THR GLU VAL SEQRES 6 B 404 LYS SER ARG PRO LYS VAL ILE THR LYS ASP PRO GLU ILE SEQRES 7 B 404 ALA ILE SER GLY ALA ASP VAL VAL ILE LEU THR VAL PRO SEQRES 8 B 404 ALA PHE ALA HIS GLU GLY TYR PHE GLN ALA MET ALA PRO SEQRES 9 B 404 TYR VAL GLN ASP SER ALA LEU ILE VAL GLY LEU PRO SER SEQRES 10 B 404 GLN ALA GLY PHE GLU PHE GLN CYS ARG ASP ILE LEU GLY SEQRES 11 B 404 ASP LYS ALA ALA ALA VAL SER MET MET SER PHE GLU THR SEQRES 12 B 404 LEU PRO TRP ALA CYS ARG ILE LYS GLU PHE GLY ARG LYS SEQRES 13 B 404 VAL GLU VAL LEU GLY THR LYS SER VAL LEU ALA ALA SER SEQRES 14 B 404 LEU ILE LYS GLY THR ALA LYS THR VAL ASP PRO LEU SER SEQRES 15 B 404 THR LEU GLN MET LEU HIS GLY ALA GLU PRO VAL PHE ARG SEQRES 16 B 404 LEU ALA LYS HIS PHE LEU GLU MET LEU ILE MET SER TYR SEQRES 17 B 404 SER PHE VAL HIS PRO ALA ILE LEU PHE GLY ARG TRP GLY SEQRES 18 B 404 SER TRP ASP GLY LYS PRO VAL PRO GLU ALA PRO LEU PHE SEQRES 19 B 404 TYR GLN GLY ILE ASP GLN ALA THR ALA ASP MET LEU THR SEQRES 20 B 404 ALA CYS SER ASN GLU CYS LYS ASP VAL ALA ASN ALA ILE SEQRES 21 B 404 MET ALA ALA CYS PRO GLY ASN ASP LEU SER ASP VAL LYS SEQRES 22 B 404 ASP ILE TYR GLN TRP TYR LEU GLU TYR TYR HIS GLU ASP SEQRES 23 B 404 ILE GLN ASP ASP HIS ASP LEU TYR HIS ALA ILE THR THR SEQRES 24 B 404 ASN LYS SER TYR LYS GLY LEU VAL HIS PRO VAL LYS ALA SEQRES 25 B 404 VAL ASP GLY GLY VAL ALA PRO ASP PHE GLY ASN ARG TYR SEQRES 26 B 404 LEU THR GLU ASP ILE PRO MET GLY MET ILE VAL PHE LYS SEQRES 27 B 404 GLY VAL ALA ILE ALA ALA GLY VAL ALA ILE PRO SER ASN SEQRES 28 B 404 ASP LYS LEU ILE MET TRP ALA GLN GLU LYS ILE GLY LYS SEQRES 29 B 404 GLU TYR LEU VAL ASP GLY ALA LEU THR GLY LYS ASP VAL SEQRES 30 B 404 ALA THR THR ARG CYS PRO GLN ARG TYR GLY PHE ASN THR SEQRES 31 B 404 LEU ASP ALA ILE LEU THR GLY LYS LYS HIS HIS HIS HIS SEQRES 32 B 404 HIS HET NAD B 405 44 HET PYR B 406 6 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM PYR PYRUVIC ACID FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 PYR C3 H4 O3 HELIX 1 1 GLY B 11 SER B 23 1 13 HELIX 2 2 ASP B 37 GLY B 47 1 11 HELIX 3 3 ASP B 75 SER B 81 1 7 HELIX 4 4 PRO B 91 PHE B 93 5 3 HELIX 5 5 ALA B 94 ALA B 103 1 10 HELIX 6 6 GLY B 120 GLY B 130 1 11 HELIX 7 7 ASP B 131 ALA B 135 5 5 HELIX 8 8 ASP B 179 GLY B 189 1 11 HELIX 9 9 HIS B 199 SER B 207 1 9 HELIX 10 10 PHE B 210 GLY B 221 1 12 HELIX 11 11 ASP B 239 CYS B 264 1 26 HELIX 12 12 ASP B 292 THR B 299 1 8 HELIX 13 13 ASN B 323 GLU B 328 1 6 HELIX 14 14 GLY B 333 GLY B 345 1 13 HELIX 15 15 ILE B 348 ILE B 362 1 15 HELIX 16 16 ASP B 376 THR B 380 5 5 HELIX 17 17 CYS B 382 GLY B 387 5 6 HELIX 18 18 THR B 390 GLY B 397 1 8 SHEET 1 A 8 VAL B 71 THR B 73 0 SHEET 2 A 8 VAL B 27 LEU B 32 1 N VAL B 31 O THR B 73 SHEET 3 A 8 VAL B 3 CYS B 8 1 N VAL B 5 O GLU B 28 SHEET 4 A 8 VAL B 85 LEU B 88 1 O VAL B 85 N CYS B 6 SHEET 5 A 8 LEU B 111 GLY B 114 1 O VAL B 113 N LEU B 88 SHEET 6 A 8 SER B 137 PHE B 141 1 O SER B 137 N ILE B 112 SHEET 7 A 8 VAL B 165 ILE B 171 -1 O SER B 169 N SER B 140 SHEET 8 A 8 VAL B 193 LEU B 196 1 O ARG B 195 N ALA B 168 SHEET 1 B 4 GLN B 62 SER B 67 0 SHEET 2 B 4 LEU B 51 ASN B 56 -1 N LEU B 51 O SER B 67 SHEET 3 B 4 LYS B 156 THR B 162 1 O VAL B 159 N ILE B 54 SHEET 4 B 4 TRP B 146 GLU B 152 -1 N ARG B 149 O GLU B 158 SHEET 1 C 2 VAL B 310 VAL B 313 0 SHEET 2 C 2 GLY B 316 PRO B 319 -1 O ALA B 318 N LYS B 311 CISPEP 1 LYS B 58 ASP B 59 0 -7.83 CISPEP 2 LEU B 115 PRO B 116 0 -19.32 CISPEP 3 PRO B 116 SER B 117 0 4.38 CISPEP 4 GLU B 191 PRO B 192 0 -6.86 CISPEP 5 TYR B 279 LEU B 280 0 0.28 CISPEP 6 HIS B 403 HIS B 404 0 4.74 SITE 1 AC1 18 GLY B 10 GLY B 11 ASN B 12 GLY B 13 SITE 2 AC1 18 PHE B 35 GLU B 38 VAL B 90 PRO B 91 SITE 3 AC1 18 PHE B 93 PRO B 116 THR B 143 LEU B 144 SITE 4 AC1 18 TRP B 146 ALA B 147 CYS B 148 ARG B 324 SITE 5 AC1 18 LYS B 398 HIS B 403 SITE 1 AC2 5 GLN B 118 THR B 143 HIS B 212 HIS B 403 SITE 2 AC2 5 HIS B 404 CRYST1 96.000 96.000 117.800 90.00 90.00 90.00 P 41 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 0.010417 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008489 0.00000