HEADER OXIDOREDUCTASE 13-AUG-96 1DXY TITLE STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-2-HYDROXYISOCAPROATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-HICDH, R-HICDH, R-2-HYDROXYISOCAPROATE DEHYDROGENASE; COMPND 5 EC: 1.1.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS CASEI; SOURCE 3 ORGANISM_TAXID: 1582; SOURCE 4 VARIANT: SSP. PSEUDOPLANTARUM; SOURCE 5 COLLECTION: DSM NUMBER: DSM 20008 (DSM = DEUTSCHE SAMMLUNG VON SOURCE 6 MIKROORGANISMEN/GERMAN COLLECTION OF MICROORGANISMS); SOURCE 7 GENE: POTENTIAL; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PJLA601 KEYWDS D-2-HYDROXYCARBOXYLATE DEHYDROGENASE, D-LACTATE DEHYDROGENASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR U.DENGLER,K.NIEFIND,M.KIESS,D.SCHOMBURG REVDAT 8 22-MAY-24 1DXY 1 REMARK REVDAT 7 09-AUG-23 1DXY 1 REMARK REVDAT 6 15-MAR-17 1DXY 1 LINK REVDAT 5 16-NOV-11 1DXY 1 HETATM REVDAT 4 13-JUL-11 1DXY 1 VERSN REVDAT 3 24-FEB-09 1DXY 1 VERSN REVDAT 2 01-APR-03 1DXY 1 JRNL REVDAT 1 16-JUN-97 1DXY 0 JRNL AUTH U.DENGLER,K.NIEFIND,M.KIESS,D.SCHOMBURG JRNL TITL CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF JRNL TITL 2 D-2-HYDROXYISOCAPROATE DEHYDROGENASE FROM LACTOBACILLUS JRNL TITL 3 CASEI, NAD+ AND 2-OXOISOCAPROATE AT 1.9 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 267 640 1997 JRNL REFN ISSN 0022-2836 JRNL PMID 9126843 JRNL DOI 10.1006/JMBI.1996.0864 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.NIEFIND,H.J.HECHT,D.SCHOMBURG REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION OF CRYSTALS REMARK 1 TITL 2 OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE FROM LACTOBACILLUS REMARK 1 TITL 3 CASEI REMARK 1 REF J.MOL.BIOL. V. 240 400 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH K.NIEFIND REMARK 1 TITL ROENTGENKRISTALLOGRAPHISCHE UNTERSUCHUNGEN AN DREI REMARK 1 TITL 2 MIKROBIELLEN ENZYMEN: D-2-HYDROXYISOCAPROAT-DEHYDROGENASE REMARK 1 TITL 3 AUS LACTOBACILLUS CASEI L-2-HYDROXYISOCAPROAT-DEHYDROGENASE REMARK 1 TITL 4 AUS LACTOBACILLUS CONFUSUS ALKALISCHE PROTEASE AUS BACILLUS REMARK 1 TITL 5 ALCALOPHILUS/VARIANTE Q59R REMARK 1 REF THESIS 1993 REMARK 1 PUBL BRAUNSCHWEIG : TECHNISCHE UNIVERSITAT BRAUNSCHWEIG (THESIS) REMARK 1 REFN REMARK 1 REFERENCE 3 REMARK 1 AUTH H.K.W.KALLWASS REMARK 1 TITL POTENTIAL OF R-2-HYDROXYISOCAPROATE DEHYDROGENASE FROM REMARK 1 TITL 2 LACTOBACILLUS CASEI FOR STEREOSPECIFIC REDUCTIONS REMARK 1 REF ENZYME.MICROB.TECHNOL. V. 14 28 1992 REMARK 1 REFN ISSN 0141-0229 REMARK 1 REFERENCE 4 REMARK 1 AUTH H.P.LERCH,H.BLOCKER,H.KALLWASS,J.HOPPE,H.TSAI,J.COLLINS REMARK 1 TITL CLONING, SEQUENCING AND EXPRESSION IN ESCHERICHIA COLI OF REMARK 1 TITL 2 THE D-2-HYDROXYISOCAPROATE DEHYDROGENASE GENE OF REMARK 1 TITL 3 LACTOBACILLUS CASEI REMARK 1 REF GENE V. 78 47 1989 REMARK 1 REFN ISSN 0378-1119 REMARK 1 REFERENCE 5 REMARK 1 AUTH H.KALLWASS,H.TSAI,H.SCHUETTE REMARK 1 TITL CRYSTALLIZATION AND MOLECULAR PROPERTIES OF REMARK 1 TITL 2 D-2-HYDROXYISOCAPROATE DEHYDROGENASE FROM LACTOBACILLUS REMARK 1 TITL 3 CASEI REMARK 1 REF FEMS MICROBIOL.LETT. V. 43 263 1987 REMARK 1 REFN ISSN 0378-1097 REMARK 1 REFERENCE 6 REMARK 1 AUTH W.HUMMEL,H.SCHUETTE,M.R.KULA REMARK 1 TITL D-2-HYDROXYISOCAPROATE DEHYDROGENASE FROM LACTOBACILLUS REMARK 1 TITL 2 CASEI. A NEW ENZYME SUITABLE FOR STEREOSPECIFIC REDUCTION OF REMARK 1 TITL 3 2-KETOCARBOXYLIC ACIDS REMARK 1 REF APPL.MICROBIOL.BIOTECHNOL. V. 21 7 1985 REMARK 1 REFN ISSN 0175-7598 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.10 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) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 53838 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2580 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.730 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.12 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.250 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 1DXY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172961. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-94 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRROR OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 12.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08900 REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.48000 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: BACKBONE AND C-BETA ATOMS OF D-GLYCERATE REMARK 200 DEHYDROGENASE (PDB ENTRY 1GDH) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.9 M AMMONIUM SULFATE, 50 MM REMARK 280 CITRATE/PHOSPHATE BUFFER, 30 MM NAD+, 60 MM 4-METHYL-2- REMARK 280 OXOPENTANOATE, PH 7.0, 277 K; ENZYME CONCENTRATION 10 MG/ML. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 62.55000 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 62.55000 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 62.55000 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 62.55000 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 62.55000 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 62.55000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: D-HICDH IS A DIMER OF IDENTICAL SUBUNITS, WHICH OCCUPIES REMARK 300 A SPECIAL POSITION IN THE INVESTIGATED CRYSTALS. 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: 8770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 -62.55000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 34670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 71660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -342.0 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 134.10000 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 67.05000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 116.13401 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 67.05000 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 116.13401 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -62.55000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 134.10000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 -62.55000 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 -62.55000 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 543 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 545 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 PRO A 331 REMARK 465 ALA A 332 REMARK 465 LYS A 333 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; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 2 CE NZ REMARK 480 LYS A 21 CE NZ REMARK 480 LYS A 43 CG CD CE NZ REMARK 480 LYS A 70 CG CD CE NZ REMARK 480 LYS A 88 CG CD CE NZ REMARK 480 LYS A 180 CD CE NZ REMARK 480 GLU A 209 CG CD OE1 OE2 REMARK 480 LYS A 321 CD CE NZ REMARK 480 GLU A 323 CG CD OE1 OE2 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 ASN A 76 -166.41 -115.43 REMARK 500 ALA A 99 59.92 -140.42 REMARK 500 SER A 101 88.51 -165.13 REMARK 500 THR A 153 46.33 -109.38 REMARK 500 HIS A 183 83.59 -163.66 REMARK 500 HIS A 204 47.73 -141.87 REMARK 500 ASN A 216 -169.56 -124.76 REMARK 500 ALA A 233 -83.74 -89.63 REMARK 500 TYR A 299 72.51 -68.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 2-OXOISOCAPROATE (OIC 337) AND A SULFATE ION (SO4 338) ARE REMARK 600 MUTUALLY EXCLUSIVELY BOUND IN THE ACTIVE SITE. THE REMARK 600 OCCUPANCY FACTORS OF BOTH LIGANDS WERE SET TO 0.5, WHILE REMARK 600 DIFFERENCES IN OCCUPATION WERE SIMULATED BY TEMPERATURE REMARK 600 FACTOR REFINEMENT. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COI A 337 REMARK 999 REMARK 999 SEQUENCE REMARK 999 A CONTACT IS OBSERVED BETWEEN THE SIDE CHAINS OF ASP 266 REMARK 999 AND ASP 278. CHEMICAL PROTEIN SEQUENCING CONFIRMED THESE REMARK 999 RESIDUES TO BE ASPARTATES. DBREF 1DXY A 1 333 UNP P17584 DHD2_LACPA 1 333 SEQRES 1 A 333 MET LYS ILE ILE ALA TYR GLY ALA ARG VAL ASP GLU ILE SEQRES 2 A 333 GLN TYR PHE LYS GLN TRP ALA LYS ASP THR GLY ASN THR SEQRES 3 A 333 LEU GLU TYR HIS THR GLU PHE LEU ASP GLU ASN THR VAL SEQRES 4 A 333 GLU TRP ALA LYS GLY PHE ASP GLY ILE ASN SER LEU GLN SEQRES 5 A 333 THR THR PRO TYR ALA ALA GLY VAL PHE GLU LYS MET HIS SEQRES 6 A 333 ALA TYR GLY ILE LYS PHE LEU THR ILE ARG ASN VAL GLY SEQRES 7 A 333 THR ASP ASN ILE ASP MET THR ALA MET LYS GLN TYR GLY SEQRES 8 A 333 ILE ARG LEU SER ASN VAL PRO ALA TYR SER PRO ALA ALA SEQRES 9 A 333 ILE ALA GLU PHE ALA LEU THR ASP THR LEU TYR LEU LEU SEQRES 10 A 333 ARG ASN MET GLY LYS VAL GLN ALA GLN LEU GLN ALA GLY SEQRES 11 A 333 ASP TYR GLU LYS ALA GLY THR PHE ILE GLY LYS GLU LEU SEQRES 12 A 333 GLY GLN GLN THR VAL GLY VAL MET GLY THR GLY HIS ILE SEQRES 13 A 333 GLY GLN VAL ALA ILE LYS LEU PHE LYS GLY PHE GLY ALA SEQRES 14 A 333 LYS VAL ILE ALA TYR ASP PRO TYR PRO MET LYS GLY ASP SEQRES 15 A 333 HIS PRO ASP PHE ASP TYR VAL SER LEU GLU ASP LEU PHE SEQRES 16 A 333 LYS GLN SER ASP VAL ILE ASP LEU HIS VAL PRO GLY ILE SEQRES 17 A 333 GLU GLN ASN THR HIS ILE ILE ASN GLU ALA ALA PHE ASN SEQRES 18 A 333 LEU MET LYS PRO GLY ALA ILE VAL ILE ASN THR ALA ARG SEQRES 19 A 333 PRO ASN LEU ILE ASP THR GLN ALA MET LEU SER ASN LEU SEQRES 20 A 333 LYS SER GLY LYS LEU ALA GLY VAL GLY ILE ASP THR TYR SEQRES 21 A 333 GLU TYR GLU THR GLU ASP LEU LEU ASN LEU ALA LYS HIS SEQRES 22 A 333 GLY SER PHE LYS ASP PRO LEU TRP ASP GLU LEU LEU GLY SEQRES 23 A 333 MET PRO ASN VAL VAL LEU SER PRO HIS ILE ALA TYR TYR SEQRES 24 A 333 THR GLU THR ALA VAL HIS ASN MET VAL TYR PHE SER LEU SEQRES 25 A 333 GLN HIS LEU VAL ASP PHE LEU THR LYS GLY GLU THR SER SEQRES 26 A 333 THR GLU VAL THR GLY PRO ALA LYS HET SO4 A 401 5 HET SO4 A 402 5 HET NAD A 403 44 HET COI A 404 9 HETNAM SO4 SULFATE ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM COI 2-OXO-4-METHYLPENTANOIC ACID HETSYN COI ALPHA-KETOISOCAPROIC ACID FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 NAD C21 H27 N7 O14 P2 FORMUL 5 COI C6 H10 O3 FORMUL 6 HOH *182(H2 O) HELIX 1 1 VAL A 10 THR A 23 5 14 HELIX 2 2 THR A 38 ALA A 42 5 5 HELIX 3 3 ALA A 58 TYR A 67 1 10 HELIX 4 4 MET A 84 GLN A 89 1 6 HELIX 5 5 PRO A 102 LEU A 117 1 16 HELIX 6 6 MET A 120 GLN A 128 1 9 HELIX 7 7 TYR A 132 GLY A 136 1 5 HELIX 8 8 LEU A 143 GLN A 145 5 3 HELIX 9 9 HIS A 155 PHE A 167 1 13 HELIX 10 10 LEU A 191 GLN A 197 1 7 HELIX 11 11 GLU A 209 ASN A 211 5 3 HELIX 12 12 GLU A 217 LEU A 222 1 6 HELIX 13 13 THR A 240 LYS A 248 1 9 HELIX 14 14 GLU A 263 HIS A 273 1 11 HELIX 15 15 PRO A 279 LEU A 285 1 7 HELIX 16 16 GLU A 301 LYS A 321 1 21 SHEET 1 A 5 THR A 26 TYR A 29 0 SHEET 2 A 5 LYS A 2 ALA A 5 1 N ILE A 3 O THR A 26 SHEET 3 A 5 GLY A 47 SER A 50 1 N GLY A 47 O ILE A 4 SHEET 4 A 5 PHE A 71 ILE A 74 1 N THR A 73 O ILE A 48 SHEET 5 A 5 ARG A 93 SER A 95 1 N ARG A 93 O LEU A 72 SHEET 1 B 6 LYS A 170 TYR A 174 0 SHEET 2 B 6 THR A 147 MET A 151 1 N VAL A 148 O LYS A 170 SHEET 3 B 6 VAL A 200 LEU A 203 1 N VAL A 200 O GLY A 149 SHEET 4 B 6 ALA A 227 ASN A 231 1 N ILE A 228 O ILE A 201 SHEET 5 B 6 LEU A 252 ILE A 257 1 N ALA A 253 O ALA A 227 SHEET 6 B 6 VAL A 290 LEU A 292 1 N VAL A 291 O VAL A 255 SITE 1 CAT 7 VAL A 77 GLY A 78 TYR A 100 THR A 232 SITE 2 CAT 7 ARG A 234 GLU A 263 HIS A 295 SITE 1 AC1 6 ASN A 76 VAL A 77 GLY A 78 TYR A 100 SITE 2 AC1 6 ARG A 234 COI A 404 SITE 1 AC2 6 PRO A 98 ALA A 99 PHE A 310 HIS A 314 SITE 2 AC2 6 THR A 326 HOH A 653 SITE 1 AC3 26 TYR A 100 GLY A 152 GLY A 154 HIS A 155 SITE 2 AC3 26 ILE A 156 TYR A 174 ASP A 175 PRO A 176 SITE 3 AC3 26 HIS A 204 VAL A 205 PRO A 206 ASN A 211 SITE 4 AC3 26 ILE A 214 THR A 232 ALA A 233 ARG A 234 SITE 5 AC3 26 ASP A 258 THR A 259 HIS A 295 TYR A 298 SITE 6 AC3 26 COI A 404 HOH A 502 HOH A 504 HOH A 580 SITE 7 AC3 26 HOH A 581 HOH A 629 SITE 1 AC4 7 VAL A 77 TYR A 100 ARG A 234 HIS A 295 SITE 2 AC4 7 MET A 307 NAD A 403 SO4 A 401 CRYST1 134.100 134.100 125.100 90.00 90.00 120.00 P 63 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 0.007457 0.004305 0.000000 0.00000 SCALE2 0.000000 0.008611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007994 0.00000