HEADER OXIDOREDUCTASE 24-FEB-13 4JDC TITLE CRYSTAL STRUCTURE OF THE DELTA-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE TITLE 2 FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.12; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RVBD_1187; SOURCE 6 EXPRESSION_SYSTEM: MYCOBACTERIUM SMEGMATIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1772; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: MC2 4517 KEYWDS PYRROLINE-5-CARBOXYLATE DEHYDROGENASE, ALDEHYDE DEHYDROGENASE, KEYWDS 2 OXYDOREDUCTION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.LAGAUTRIERE,G.BASHIRI,E.N.BAKER REVDAT 3 15-NOV-17 4JDC 1 REMARK REVDAT 2 16-APR-14 4JDC 1 JRNL REVDAT 1 18-DEC-13 4JDC 0 JRNL AUTH T.LAGAUTRIERE,G.BASHIRI,N.G.PATERSON,M.BERNEY,G.M.COOK, JRNL AUTH 2 E.N.BAKER JRNL TITL CHARACTERIZATION OF THE PROLINE-UTILIZATION PATHWAY IN JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS THROUGH STRUCTURAL AND FUNCTIONAL JRNL TITL 3 STUDIES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 968 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24699642 JRNL DOI 10.1107/S1399004713034391 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 93414 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4908 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6205 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 334 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4108 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 389 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : -0.21000 REMARK 3 B12 (A**2) : 0.07000 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): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.434 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4242 ; 0.028 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5791 ; 2.644 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 6.642 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;35.725 ;22.969 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 622 ;13.203 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;23.558 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 642 ; 0.207 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3298 ; 0.017 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4JDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000077903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953688 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 93414 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE/TRIS PH 8.1, 12% REMARK 280 POLYETHYLENE GLYCOL (PEG) 1000, 12% PEG 3350, 12% 2-METHYL-2,4- REMARK 280 PENTANDIOL (MPD), 0.03 M SODIUM NITRATE, 0.03 M DISODIUM REMARK 280 HYDROGEN PHOSPHATE AND 0.03 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 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 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 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 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 96.18100 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 44630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 97850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL 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 -0.500000 -0.866025 0.000000 163.13300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 81.56650 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 141.27732 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 81.56650 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 141.27732 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 96.18100 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 163.13300 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 96.18100 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 96.18100 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 898 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1006 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 ASP A 419 REMARK 465 GLU A 420 REMARK 465 SER A 421 REMARK 465 PHE A 422 REMARK 465 VAL A 423 REMARK 465 ILE A 424 REMARK 465 GLU A 425 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 HIS A 44 CG HIS A 44 CD2 0.055 REMARK 500 HIS A 64 CG HIS A 64 CD2 0.070 REMARK 500 HIS A 78 CG HIS A 78 CD2 0.065 REMARK 500 TRP A 95 CE2 TRP A 95 CD2 0.084 REMARK 500 HIS A 272 CG HIS A 272 CD2 0.065 REMARK 500 TRP A 274 CE2 TRP A 274 CD2 0.074 REMARK 500 SER A 363 CA SER A 363 CB 0.100 REMARK 500 GLU A 439 CD GLU A 439 OE1 0.110 REMARK 500 ASN A 507 CG ASN A 507 ND2 0.152 REMARK 500 TRP A 519 CE2 TRP A 519 CD2 0.084 REMARK 500 HIS A 539 CG HIS A 539 CD2 0.057 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 25 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 25 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 41 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 244 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 307 NE - CZ - NH1 ANGL. DEV. = -9.6 DEGREES REMARK 500 ARG A 307 NE - CZ - NH2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 361 CB - CG - OD1 ANGL. DEV. = 9.6 DEGREES REMARK 500 ASP A 361 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 GLY A 500 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 ARG A 518 NE - CZ - NH2 ANGL. DEV. = -3.3 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 LYS A 21 -9.02 84.41 REMARK 500 ARG A 65 73.26 -164.33 REMARK 500 ASP A 140 -73.58 -97.77 REMARK 500 VAL A 142 -71.76 -105.97 REMARK 500 ASP A 400 118.96 -165.28 REMARK 500 SER A 452 32.89 -87.58 REMARK 500 ALA A 462 131.45 -172.01 REMARK 500 PRO A 488 37.22 -90.30 REMARK 500 PRO A 497 -179.49 -68.60 REMARK 500 PHE A 498 -157.48 64.44 REMARK 500 PHE A 498 -156.48 64.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAD A 601 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IHI RELATED DB: PDB REMARK 900 PRUA-NAD (LONG UNIT CELL) REMARK 900 RELATED ID: 4IDM RELATED DB: PDB REMARK 900 SEMET-PRUA (SHORT UNIT CELL) REMARK 900 RELATED ID: 4IDS RELATED DB: PDB REMARK 900 APO-PRUA (LONG UNIT CELL) DBREF 4JDC A 1 543 UNP I6X0K4 I6X0K4_MYCTU 1 543 SEQADV 4JDC MET A -19 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC GLY A -18 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC SER A -17 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC SER A -16 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC HIS A -15 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC HIS A -14 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC HIS A -13 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC HIS A -12 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC HIS A -11 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC HIS A -10 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC SER A -9 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC SER A -8 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC GLY A -7 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC LEU A -6 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC VAL A -5 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC PRO A -4 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC ARG A -3 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC GLY A -2 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC SER A -1 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC HIS A 0 UNP I6X0K4 EXPRESSION TAG SEQADV 4JDC ASP A 505 UNP I6X0K4 GLY 505 ENGINEERED MUTATION SEQRES 1 A 563 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 563 LEU VAL PRO ARG GLY SER HIS MET ASP ALA ILE THR GLN SEQRES 3 A 563 VAL PRO VAL PRO ALA ASN GLU PRO VAL HIS ASP TYR ALA SEQRES 4 A 563 PRO LYS SER PRO GLU ARG THR ARG LEU ARG THR GLU LEU SEQRES 5 A 563 ALA SER LEU ALA ASP HIS PRO ILE ASP LEU PRO HIS VAL SEQRES 6 A 563 ILE GLY GLY ARG HIS ARG MET GLY ASP GLY GLU ARG ILE SEQRES 7 A 563 ASP VAL VAL GLN PRO HIS ARG HIS ALA ALA ARG LEU GLY SEQRES 8 A 563 THR LEU THR ASN ALA THR HIS ALA ASP ALA ALA ALA ALA SEQRES 9 A 563 VAL GLU ALA ALA MET SER ALA LYS SER ASP TRP ALA ALA SEQRES 10 A 563 LEU PRO PHE ASP GLU ARG ALA ALA VAL PHE LEU ARG ALA SEQRES 11 A 563 ALA ASP LEU LEU ALA GLY PRO TRP ARG GLU LYS ILE ALA SEQRES 12 A 563 ALA ALA THR MET LEU GLY GLN SER LYS SER VAL TYR GLN SEQRES 13 A 563 ALA GLU ILE ASP ALA VAL CYS GLU LEU ILE ASP PHE TRP SEQRES 14 A 563 ARG PHE ASN VAL ALA PHE ALA ARG GLN ILE LEU GLU GLN SEQRES 15 A 563 GLN PRO ILE SER GLY PRO GLY GLU TRP ASN ARG ILE ASP SEQRES 16 A 563 TYR ARG PRO LEU ASP GLY PHE VAL TYR ALA ILE THR PRO SEQRES 17 A 563 PHE ASN PHE THR SER ILE ALA GLY ASN LEU PRO THR ALA SEQRES 18 A 563 PRO ALA LEU MET GLY ASN THR VAL ILE TRP LYS PRO SER SEQRES 19 A 563 ILE THR GLN THR LEU ALA ALA TYR LEU THR MET GLN LEU SEQRES 20 A 563 LEU GLU ALA ALA GLY LEU PRO PRO GLY VAL ILE ASN LEU SEQRES 21 A 563 VAL THR GLY ASP GLY PHE ALA VAL SER ASP VAL ALA LEU SEQRES 22 A 563 ALA ASP PRO ARG LEU ALA GLY ILE HIS PHE THR GLY SER SEQRES 23 A 563 THR ALA THR PHE GLY HIS LEU TRP GLN TRP VAL GLY THR SEQRES 24 A 563 ASN ILE GLY ARG TYR HIS SER TYR PRO ARG LEU VAL GLY SEQRES 25 A 563 GLU THR GLY GLY LYS ASP PHE VAL VAL ALA HIS ALA SER SEQRES 26 A 563 ALA ARG PRO ASP VAL LEU ARG THR ALA LEU ILE ARG GLY SEQRES 27 A 563 ALA PHE ASP TYR GLN GLY GLN LYS CME SER ALA VAL SER SEQRES 28 A 563 ARG ALA PHE ILE ALA HIS SER VAL TRP GLN ARG MET GLY SEQRES 29 A 563 ASP GLU LEU LEU ALA LYS ALA ALA GLU LEU ARG TYR GLY SEQRES 30 A 563 ASP ILE THR ASP LEU SER ASN TYR GLY GLY ALA LEU ILE SEQRES 31 A 563 ASP GLN ARG ALA PHE VAL LYS ASN VAL ASP ALA ILE GLU SEQRES 32 A 563 ARG ALA LYS GLY ALA ALA ALA VAL THR VAL ALA VAL GLY SEQRES 33 A 563 GLY GLU TYR ASP ASP SER GLU GLY TYR PHE VAL ARG PRO SEQRES 34 A 563 THR VAL LEU LEU SER ASP ASP PRO THR ASP GLU SER PHE SEQRES 35 A 563 VAL ILE GLU TYR PHE GLY PRO LEU LEU SER VAL HIS VAL SEQRES 36 A 563 TYR PRO ASP GLU ARG TYR GLU GLN ILE LEU ASP VAL ILE SEQRES 37 A 563 ASP THR GLY SER ARG TYR ALA LEU THR GLY ALA VAL ILE SEQRES 38 A 563 ALA ASP ASP ARG GLN ALA VAL LEU THR ALA LEU ASP ARG SEQRES 39 A 563 LEU ARG PHE ALA ALA GLY ASN PHE TYR VAL ASN ASP LYS SEQRES 40 A 563 PRO THR GLY ALA VAL VAL GLY ARG GLN PRO PHE GLY GLY SEQRES 41 A 563 ALA ARG GLY SER ASP THR ASN ASP LYS ALA GLY SER PRO SEQRES 42 A 563 LEU ASN LEU LEU ARG TRP THR SER ALA ARG SER ILE LYS SEQRES 43 A 563 GLU THR PHE VAL ALA ALA THR ASP HIS ILE TYR PRO HIS SEQRES 44 A 563 MET ALA VAL ASP MODRES 4JDC CME A 327 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET CME A 327 10 HET NAD A 601 27 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 1 CME C5 H11 N O3 S2 FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 HOH *389(H2 O) HELIX 1 1 SER A 22 HIS A 38 1 17 HELIX 2 2 THR A 77 ALA A 97 1 21 HELIX 3 3 PRO A 99 GLY A 116 1 18 HELIX 4 4 TRP A 118 SER A 131 1 14 HELIX 5 5 SER A 133 ALA A 141 1 9 HELIX 6 6 VAL A 142 GLU A 161 1 20 HELIX 7 7 PHE A 191 MET A 205 1 15 HELIX 8 8 SER A 214 THR A 216 5 3 HELIX 9 9 GLN A 217 ALA A 231 1 15 HELIX 10 10 GLY A 245 LEU A 253 1 9 HELIX 11 11 SER A 266 ASN A 280 1 15 HELIX 12 12 ILE A 281 TYR A 284 5 4 HELIX 13 13 ARG A 307 ASP A 321 1 15 HELIX 14 14 TYR A 322 GLN A 325 5 4 HELIX 15 15 HIS A 337 LEU A 354 1 18 HELIX 16 16 ASP A 371 ALA A 388 1 18 HELIX 17 17 PRO A 437 GLU A 439 5 3 HELIX 18 18 ARG A 440 GLY A 451 1 12 HELIX 19 19 ASP A 464 LEU A 475 1 12 HELIX 20 20 SER A 512 TRP A 519 1 8 HELIX 21 21 TYR A 537 ALA A 541 5 5 SHEET 1 A 3 ILE A 40 LEU A 42 0 SHEET 2 A 3 ARG A 65 THR A 74 1 O THR A 72 N LEU A 42 SHEET 3 A 3 ARG A 57 GLN A 62 -1 N VAL A 60 O LEU A 70 SHEET 1 B 2 HIS A 44 ILE A 46 0 SHEET 2 B 2 ARG A 49 ARG A 51 -1 O ARG A 51 N HIS A 44 SHEET 1 C 2 GLU A 170 PRO A 178 0 SHEET 2 C 2 THR A 520 THR A 528 -1 O ILE A 525 N ARG A 173 SHEET 1 D 5 ILE A 238 LEU A 240 0 SHEET 2 D 5 VAL A 209 LYS A 212 1 N TRP A 211 O ASN A 239 SHEET 3 D 5 PHE A 182 ILE A 186 1 N ALA A 185 O ILE A 210 SHEET 4 D 5 LEU A 258 GLY A 265 1 O ALA A 259 N PHE A 182 SHEET 5 D 5 ARG A 289 THR A 294 1 O VAL A 291 N ILE A 261 SHEET 1 E 7 VAL A 391 VAL A 395 0 SHEET 2 E 7 THR A 410 SER A 414 -1 O LEU A 413 N THR A 392 SHEET 3 E 7 LEU A 430 TYR A 436 1 O VAL A 433 N LEU A 412 SHEET 4 E 7 VAL A 330 ALA A 336 1 N ALA A 333 O HIS A 434 SHEET 5 E 7 LYS A 297 ALA A 302 1 N ALA A 302 O PHE A 334 SHEET 6 E 7 ALA A 455 ILE A 461 1 O ILE A 461 N VAL A 301 SHEET 7 E 7 ASN A 481 VAL A 484 1 O TYR A 483 N VAL A 460 SHEET 1 F 2 TYR A 399 ASP A 400 0 SHEET 2 F 2 PHE A 406 VAL A 407 -1 O PHE A 406 N ASP A 400 LINK C LYS A 326 N CME A 327 1555 1555 1.33 LINK C CME A 327 N SER A 328 1555 1555 1.32 CISPEP 1 VAL A 542 ASP A 543 0 -5.35 SITE 1 AC1 18 TYR A 184 ILE A 186 THR A 187 PRO A 188 SITE 2 AC1 18 PHE A 189 LYS A 212 PRO A 213 SER A 214 SITE 3 AC1 18 GLY A 245 PHE A 246 SER A 249 GLY A 265 SITE 4 AC1 18 SER A 266 THR A 269 CME A 327 HOH A 763 SITE 5 AC1 18 HOH A 936 HOH A 938 CRYST1 163.133 163.133 96.181 90.00 90.00 120.00 P 6 2 2 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 0.006130 0.003539 0.000000 0.00000 SCALE2 0.000000 0.007078 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010397 0.00000