HEADER OXIDOREDUCTASE 13-APR-99 3HDH TITLE PIG HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE REVISITED: TITLE 2 SEQUENCE ANALYSIS AND CRYSTAL STRUCTURE DETERMINATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE); COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: SCHAD; COMPND 5 EC: 1.1.1.35 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 ORGAN: HEART; SOURCE 6 ORGANELLE: MITOCHONDRIAL KEYWDS OXIDOREDUCTASE, BETA OXIDATION, SCHAD, CATALYTIC ACTIVITY: L-3- KEYWDS 2 HYDROXYACYL-COA + NAD(+) = 3-OXOACYL-COA + NADH EXPDTA X-RAY DIFFRACTION AUTHOR J.J.BARYCKI,L.K.O'BRIEN,J.J.BIRKTOFT,A.W.STRAUSS,L.J.BANASZAK REVDAT 5 02-AUG-23 3HDH 1 REMARK REVDAT 4 24-FEB-09 3HDH 1 VERSN REVDAT 3 01-APR-03 3HDH 1 JRNL REVDAT 2 26-SEP-01 3HDH 3 ATOM REVDAT 1 08-OCT-99 3HDH 0 JRNL AUTH J.J.BARYCKI,L.K.O'BRIEN,J.J.BIRKTOFT,A.W.STRAUSS, JRNL AUTH 2 L.J.BANASZAK JRNL TITL PIG HEART SHORT CHAIN L-3-HYDROXYACYL-COA DEHYDROGENASE JRNL TITL 2 REVISITED: SEQUENCE ANALYSIS AND CRYSTAL STRUCTURE JRNL TITL 3 DETERMINATION. JRNL REF PROTEIN SCI. V. 8 2010 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10548046 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.J.BIRKTOFT,H.M.HOLDEN,R.HAMLIN,N.H.XUONG,L.J.BANASZAK REMARK 1 TITL STRUCTURE OF L-3-HYDROXYACYL-COENZYME A DEHYDROGENASE: REMARK 1 TITL 2 PRELIMINARY CHAIN TRACING AT 2.8-A RESOLUTION REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 84 8262 1987 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.7 REMARK 3 NUMBER OF REFLECTIONS : 24618 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) : 0.223 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1201 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2850 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 160 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6506 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 132 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.44 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) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 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) : 3.100 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.070 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.770 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.140 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NAD.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NAD.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 3 REMARK 3 POOR ELECTRON DENSITY OBSERVED FOR THIRD SUBUNIT (SUBUNIT REMARK 3 C). THREE BREAKS WERE OBSERVED IN THE DENSITY AND SEVERAL REMARK 3 RESIDUES HAVE BEEN ASSIGNED OCCUPANCIES OF 0.5 REMARK 4 REMARK 4 3HDH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-85 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 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 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3HAD REMARK 200 REMARK 200 REMARK: USED DIMER AS A PROBE. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM TRIS, PH 8.0, + 1MM DTT + 11-14% REMARK 280 PEG 6K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 62.35000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.35000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 113.60000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.05000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 113.60000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.05000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 62.35000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 113.60000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.05000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 62.35000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 113.60000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.05000 REMARK 290 SMTRY3 8 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 300 REMARK: UNUSUAL SITUATION OF 3 SUBUNITS CONTAINED WITHIN THE REMARK 300 ASYMMETRIC UNIT FOR A DIMERIC ENZYME. 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: 5300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 62.35000 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 SER A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 SER A 9 REMARK 465 ALA A 10 REMARK 465 LYS A 11 REMARK 465 SER B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 THR B 5 REMARK 465 ALA B 6 REMARK 465 ALA B 7 REMARK 465 ALA B 8 REMARK 465 SER B 9 REMARK 465 ALA B 10 REMARK 465 LYS B 11 REMARK 465 SER C 1 REMARK 465 SER C 2 REMARK 465 SER C 3 REMARK 465 SER C 4 REMARK 465 THR C 5 REMARK 465 ALA C 6 REMARK 465 ALA C 7 REMARK 465 ALA C 8 REMARK 465 SER C 9 REMARK 465 ALA C 10 REMARK 465 LYS C 11 REMARK 465 ARG C 224 REMARK 465 GLY C 225 REMARK 465 ASP C 226 REMARK 465 ALA C 227 REMARK 465 SER C 228 REMARK 465 GLY C 241 REMARK 465 TYR C 242 REMARK 465 PRO C 243 REMARK 465 MET C 244 REMARK 465 MET C 268 REMARK 465 ASP C 269 REMARK 465 SER C 270 REMARK 465 GLN C 271 REMARK 465 ASN C 272 REMARK 465 PRO C 273 REMARK 465 LEU C 274 REMARK 465 PHE C 275 REMARK 465 GLN C 276 REMARK 465 PRO C 277 REMARK 465 GLU C 296 REMARK 465 GLY C 297 REMARK 465 PHE C 298 REMARK 465 TYR C 299 REMARK 465 LYS C 300 REMARK 465 TYR C 301 REMARK 465 LYS C 302 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 LYS B 302 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASP C 231 N ALA C 235 2.15 REMARK 500 O ALA C 235 N GLY C 239 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 CG GLU C 217 CG GLU C 217 3555 2.06 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 PRO A 196 C - N - CA ANGL. DEV. = 10.4 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 LEU A 25 -72.23 -34.40 REMARK 500 ALA A 36 -25.21 -39.02 REMARK 500 ASN A 73 78.70 175.08 REMARK 500 THR A 84 -72.26 -46.90 REMARK 500 SER A 87 0.62 -64.92 REMARK 500 ALA A 95 -32.57 -37.15 REMARK 500 ALA A 107 68.09 -159.36 REMARK 500 VAL A 109 131.80 -28.18 REMARK 500 ALA A 126 155.51 -48.65 REMARK 500 GLN A 151 -35.97 -34.55 REMARK 500 PHE A 205 -115.62 60.70 REMARK 500 VAL A 207 -70.93 -50.85 REMARK 500 MET A 268 16.21 -61.44 REMARK 500 ASP A 269 77.73 165.44 REMARK 500 LYS A 283 -77.46 -72.58 REMARK 500 LEU A 284 -38.10 -37.55 REMARK 500 ALA A 286 -0.92 -57.92 REMARK 500 VAL B 15 107.73 -44.84 REMARK 500 GLN B 32 -80.22 -47.46 REMARK 500 VAL B 33 -34.12 -39.38 REMARK 500 ALA B 34 -73.90 -64.57 REMARK 500 ALA B 36 -16.85 -46.02 REMARK 500 ASP B 45 -157.45 -157.82 REMARK 500 ALA B 66 -73.92 -135.47 REMARK 500 GLU B 72 -94.32 -47.35 REMARK 500 ALA B 76 51.13 -64.06 REMARK 500 SER B 87 56.91 -105.92 REMARK 500 ILE B 88 85.60 -150.16 REMARK 500 SER B 89 -168.55 -60.69 REMARK 500 LEU B 103 119.54 -166.34 REMARK 500 ALA B 107 62.67 -151.30 REMARK 500 VAL B 109 140.80 -36.65 REMARK 500 LYS B 124 -76.34 -74.49 REMARK 500 GLU B 128 -79.89 -72.80 REMARK 500 HIS B 129 -38.01 -38.00 REMARK 500 THR B 130 133.05 -36.22 REMARK 500 LYS B 200 -177.27 -61.15 REMARK 500 PHE B 205 -117.48 50.66 REMARK 500 ILE B 206 -78.05 -104.02 REMARK 500 VAL B 207 -80.59 -39.23 REMARK 500 PHE B 260 -80.57 -38.15 REMARK 500 MET B 268 -6.64 -59.53 REMARK 500 ASP B 269 78.21 -176.25 REMARK 500 GLN B 276 109.65 -57.94 REMARK 500 LYS B 293 11.86 -66.28 REMARK 500 THR B 294 -8.99 -142.78 REMARK 500 LEU C 25 -72.94 -40.66 REMARK 500 GLN C 46 -70.98 -66.22 REMARK 500 THR C 47 -167.65 -77.26 REMARK 500 ASN C 73 70.01 -167.91 REMARK 500 REMARK 500 THIS ENTRY HAS 66 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR C 222 0.07 SIDE CHAIN 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 A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 750 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD C 1150 DBREF 3HDH A 1 302 UNP P00348 HCDH_PIG 1 302 DBREF 3HDH B 1 302 UNP P00348 HCDH_PIG 1 302 DBREF 3HDH C 1 302 UNP P00348 HCDH_PIG 1 302 SEQRES 1 A 302 SER SER SER SER THR ALA ALA ALA SER ALA LYS LYS ILE SEQRES 2 A 302 LEU VAL LYS HIS VAL THR VAL ILE GLY GLY GLY LEU MET SEQRES 3 A 302 GLY ALA GLY ILE ALA GLN VAL ALA ALA ALA THR GLY HIS SEQRES 4 A 302 THR VAL VAL LEU VAL ASP GLN THR GLU ASP ILE LEU ALA SEQRES 5 A 302 LYS SER LYS LYS GLY ILE GLU GLU SER LEU ARG LYS VAL SEQRES 6 A 302 ALA LYS LYS LYS PHE ALA GLU ASN PRO LYS ALA GLY ASP SEQRES 7 A 302 GLU PHE VAL GLU LYS THR LEU SER SER ILE SER THR SER SEQRES 8 A 302 THR ASP ALA ALA SER VAL VAL HIS SER THR ASP LEU VAL SEQRES 9 A 302 VAL GLU ALA ILE VAL GLU ASN LEU LYS VAL LYS SER GLU SEQRES 10 A 302 LEU PHE LYS ARG LEU ASP LYS PHE ALA ALA GLU HIS THR SEQRES 11 A 302 ILE PHE ALA SER ASN THR SER SER LEU GLN ILE THR SER SEQRES 12 A 302 LEU ALA ASN ALA THR THR ARG GLN ASP ARG PHE ALA GLY SEQRES 13 A 302 LEU HIS PHE PHE ASN PRO VAL PRO LEU MET LYS LEU VAL SEQRES 14 A 302 GLU VAL VAL LYS THR PRO MET THR SER GLN LYS THR LEU SEQRES 15 A 302 GLU SER LEU VAL ASP PHE SER LYS THR LEU GLY LYS HIS SEQRES 16 A 302 PRO VAL SER CYS LYS ASP THR PRO GLY PHE ILE VAL ASN SEQRES 17 A 302 ARG LEU LEU VAL PRO TYR LEU ILE GLU ALA VAL ARG LEU SEQRES 18 A 302 TYR GLU ARG GLY ASP ALA SER LYS GLU ASP ILE ASP THR SEQRES 19 A 302 ALA MET LYS LEU GLY ALA GLY TYR PRO MET GLY PRO PHE SEQRES 20 A 302 GLU LEU LEU ASP TYR VAL GLY LEU ASP THR THR LYS PHE SEQRES 21 A 302 ILE ILE ASP GLY TRP HIS GLU MET ASP SER GLN ASN PRO SEQRES 22 A 302 LEU PHE GLN PRO SER PRO ALA MET ASN LYS LEU VAL ALA SEQRES 23 A 302 GLU ASN LYS PHE GLY LYS LYS THR GLY GLU GLY PHE TYR SEQRES 24 A 302 LYS TYR LYS SEQRES 1 B 302 SER SER SER SER THR ALA ALA ALA SER ALA LYS LYS ILE SEQRES 2 B 302 LEU VAL LYS HIS VAL THR VAL ILE GLY GLY GLY LEU MET SEQRES 3 B 302 GLY ALA GLY ILE ALA GLN VAL ALA ALA ALA THR GLY HIS SEQRES 4 B 302 THR VAL VAL LEU VAL ASP GLN THR GLU ASP ILE LEU ALA SEQRES 5 B 302 LYS SER LYS LYS GLY ILE GLU GLU SER LEU ARG LYS VAL SEQRES 6 B 302 ALA LYS LYS LYS PHE ALA GLU ASN PRO LYS ALA GLY ASP SEQRES 7 B 302 GLU PHE VAL GLU LYS THR LEU SER SER ILE SER THR SER SEQRES 8 B 302 THR ASP ALA ALA SER VAL VAL HIS SER THR ASP LEU VAL SEQRES 9 B 302 VAL GLU ALA ILE VAL GLU ASN LEU LYS VAL LYS SER GLU SEQRES 10 B 302 LEU PHE LYS ARG LEU ASP LYS PHE ALA ALA GLU HIS THR SEQRES 11 B 302 ILE PHE ALA SER ASN THR SER SER LEU GLN ILE THR SER SEQRES 12 B 302 LEU ALA ASN ALA THR THR ARG GLN ASP ARG PHE ALA GLY SEQRES 13 B 302 LEU HIS PHE PHE ASN PRO VAL PRO LEU MET LYS LEU VAL SEQRES 14 B 302 GLU VAL VAL LYS THR PRO MET THR SER GLN LYS THR LEU SEQRES 15 B 302 GLU SER LEU VAL ASP PHE SER LYS THR LEU GLY LYS HIS SEQRES 16 B 302 PRO VAL SER CYS LYS ASP THR PRO GLY PHE ILE VAL ASN SEQRES 17 B 302 ARG LEU LEU VAL PRO TYR LEU ILE GLU ALA VAL ARG LEU SEQRES 18 B 302 TYR GLU ARG GLY ASP ALA SER LYS GLU ASP ILE ASP THR SEQRES 19 B 302 ALA MET LYS LEU GLY ALA GLY TYR PRO MET GLY PRO PHE SEQRES 20 B 302 GLU LEU LEU ASP TYR VAL GLY LEU ASP THR THR LYS PHE SEQRES 21 B 302 ILE ILE ASP GLY TRP HIS GLU MET ASP SER GLN ASN PRO SEQRES 22 B 302 LEU PHE GLN PRO SER PRO ALA MET ASN LYS LEU VAL ALA SEQRES 23 B 302 GLU ASN LYS PHE GLY LYS LYS THR GLY GLU GLY PHE TYR SEQRES 24 B 302 LYS TYR LYS SEQRES 1 C 302 SER SER SER SER THR ALA ALA ALA SER ALA LYS LYS ILE SEQRES 2 C 302 LEU VAL LYS HIS VAL THR VAL ILE GLY GLY GLY LEU MET SEQRES 3 C 302 GLY ALA GLY ILE ALA GLN VAL ALA ALA ALA THR GLY HIS SEQRES 4 C 302 THR VAL VAL LEU VAL ASP GLN THR GLU ASP ILE LEU ALA SEQRES 5 C 302 LYS SER LYS LYS GLY ILE GLU GLU SER LEU ARG LYS VAL SEQRES 6 C 302 ALA LYS LYS LYS PHE ALA GLU ASN PRO LYS ALA GLY ASP SEQRES 7 C 302 GLU PHE VAL GLU LYS THR LEU SER SER ILE SER THR SER SEQRES 8 C 302 THR ASP ALA ALA SER VAL VAL HIS SER THR ASP LEU VAL SEQRES 9 C 302 VAL GLU ALA ILE VAL GLU ASN LEU LYS VAL LYS SER GLU SEQRES 10 C 302 LEU PHE LYS ARG LEU ASP LYS PHE ALA ALA GLU HIS THR SEQRES 11 C 302 ILE PHE ALA SER ASN THR SER SER LEU GLN ILE THR SER SEQRES 12 C 302 LEU ALA ASN ALA THR THR ARG GLN ASP ARG PHE ALA GLY SEQRES 13 C 302 LEU HIS PHE PHE ASN PRO VAL PRO LEU MET LYS LEU VAL SEQRES 14 C 302 GLU VAL VAL LYS THR PRO MET THR SER GLN LYS THR LEU SEQRES 15 C 302 GLU SER LEU VAL ASP PHE SER LYS THR LEU GLY LYS HIS SEQRES 16 C 302 PRO VAL SER CYS LYS ASP THR PRO GLY PHE ILE VAL ASN SEQRES 17 C 302 ARG LEU LEU VAL PRO TYR LEU ILE GLU ALA VAL ARG LEU SEQRES 18 C 302 TYR GLU ARG GLY ASP ALA SER LYS GLU ASP ILE ASP THR SEQRES 19 C 302 ALA MET LYS LEU GLY ALA GLY TYR PRO MET GLY PRO PHE SEQRES 20 C 302 GLU LEU LEU ASP TYR VAL GLY LEU ASP THR THR LYS PHE SEQRES 21 C 302 ILE ILE ASP GLY TRP HIS GLU MET ASP SER GLN ASN PRO SEQRES 22 C 302 LEU PHE GLN PRO SER PRO ALA MET ASN LYS LEU VAL ALA SEQRES 23 C 302 GLU ASN LYS PHE GLY LYS LYS THR GLY GLU GLY PHE TYR SEQRES 24 C 302 LYS TYR LYS HET NAD A 350 44 HET NAD B 750 44 HET NAD C1150 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 4 NAD 3(C21 H27 N7 O14 P2) FORMUL 7 HOH *23(H2 O) HELIX 1 1 LEU A 25 ALA A 36 1 12 HELIX 2 2 GLU A 48 LYS A 69 1 22 HELIX 3 3 PRO A 74 SER A 87 1 14 HELIX 4 4 ALA A 94 SER A 96 5 3 HELIX 5 5 LEU A 112 PHE A 125 1 14 HELIX 6 6 ILE A 141 ALA A 147 1 7 HELIX 7 7 GLN A 151 ARG A 153 5 3 HELIX 8 8 GLN A 179 THR A 191 1 13 HELIX 9 9 VAL A 207 GLU A 223 1 17 HELIX 10 10 LYS A 229 ALA A 240 1 12 HELIX 11 11 PRO A 246 VAL A 253 1 8 HELIX 12 12 LEU A 255 ASP A 269 1 15 HELIX 13 13 PRO A 273 PHE A 275 5 3 HELIX 14 14 PRO A 279 ALA A 286 1 8 HELIX 15 15 LEU B 25 THR B 37 1 13 HELIX 16 16 GLU B 48 LYS B 64 1 17 HELIX 17 17 PHE B 80 SER B 86 1 7 HELIX 18 18 LEU B 112 PHE B 125 1 14 HELIX 19 19 ILE B 141 ALA B 147 1 7 HELIX 20 20 GLN B 151 ARG B 153 5 3 HELIX 21 21 GLN B 179 LEU B 192 1 14 HELIX 22 22 VAL B 207 ARG B 224 1 18 HELIX 23 23 LYS B 229 GLY B 239 1 11 HELIX 24 24 PRO B 246 VAL B 253 1 8 HELIX 25 25 LEU B 255 ASP B 269 1 15 HELIX 26 26 PRO B 279 GLU B 287 1 9 HELIX 27 27 LYS B 292 THR B 294 5 3 HELIX 28 28 LEU C 25 ALA C 36 1 12 HELIX 29 29 ILE C 50 LYS C 69 1 20 HELIX 30 30 PRO C 74 SER C 87 1 14 HELIX 31 31 ALA C 94 SER C 96 5 3 HELIX 32 32 LEU C 112 PHE C 125 1 14 HELIX 33 33 ILE C 141 ALA C 147 1 7 HELIX 34 34 GLN C 151 ARG C 153 5 3 HELIX 35 35 GLN C 179 THR C 191 1 13 HELIX 36 36 VAL C 207 TYR C 222 1 16 HELIX 37 37 ASP C 231 GLY C 239 1 9 HELIX 38 38 PRO C 246 VAL C 253 1 8 HELIX 39 39 PHE C 260 TRP C 265 1 6 SHEET 1 A 8 HIS A 195 LYS A 200 0 SHEET 2 A 8 LEU A 168 LYS A 173 1 N VAL A 169 O HIS A 195 SHEET 3 A 8 PHE A 154 PHE A 159 -1 N HIS A 158 O GLU A 170 SHEET 4 A 8 ILE A 131 SER A 134 1 N PHE A 132 O ALA A 155 SHEET 5 A 8 LEU A 103 GLU A 106 1 N VAL A 104 O ILE A 131 SHEET 6 A 8 HIS A 17 ILE A 21 1 N THR A 19 O LEU A 103 SHEET 7 A 8 THR A 40 VAL A 44 1 N THR A 40 O VAL A 18 SHEET 8 A 8 ILE A 88 SER A 91 1 N SER A 89 O VAL A 41 SHEET 1 B 6 THR B 19 ILE B 21 0 SHEET 2 B 6 LEU B 103 GLU B 106 1 N VAL B 105 O THR B 19 SHEET 3 B 6 ILE B 131 SER B 134 1 N ILE B 131 O VAL B 104 SHEET 4 B 6 PHE B 154 PHE B 159 1 N ALA B 155 O PHE B 132 SHEET 5 B 6 LEU B 168 VAL B 172 -1 N VAL B 172 O GLY B 156 SHEET 6 B 6 HIS B 195 CYS B 199 1 N HIS B 195 O VAL B 169 SHEET 1 C 2 VAL B 41 VAL B 44 0 SHEET 2 C 2 ILE B 88 SER B 91 1 N SER B 89 O VAL B 41 SHEET 1 D 5 ILE C 131 SER C 134 0 SHEET 2 D 5 LEU C 103 GLU C 106 1 N VAL C 104 O ILE C 131 SHEET 3 D 5 HIS C 17 ILE C 21 1 N THR C 19 O LEU C 103 SHEET 4 D 5 THR C 40 VAL C 44 1 N THR C 40 O VAL C 18 SHEET 5 D 5 ILE C 88 SER C 91 1 N SER C 89 O VAL C 41 SHEET 1 E 3 ALA C 155 HIS C 158 0 SHEET 2 E 3 LEU C 168 LYS C 173 -1 N VAL C 172 O GLY C 156 SHEET 3 E 3 HIS C 195 LYS C 200 1 N HIS C 195 O VAL C 169 CISPEP 1 ASN A 161 PRO A 162 0 -0.61 CISPEP 2 ASN B 161 PRO B 162 0 0.88 CISPEP 3 ASN C 161 PRO C 162 0 -1.01 SITE 1 AC1 14 LEU A 25 MET A 26 ASP A 45 GLN A 46 SITE 2 AC1 14 ALA A 107 ILE A 108 VAL A 109 GLU A 110 SITE 3 AC1 14 VAL A 114 LYS A 115 ASN A 135 SER A 137 SITE 4 AC1 14 HIS A 158 PHE A 159 SITE 1 AC2 12 GLY B 24 LEU B 25 MET B 26 ASP B 45 SITE 2 AC2 12 GLN B 46 ALA B 107 ILE B 108 GLU B 110 SITE 3 AC2 12 LYS B 115 ASN B 135 SER B 137 PHE B 159 SITE 1 AC3 16 GLY C 22 LEU C 25 MET C 26 ASP C 45 SITE 2 AC3 16 GLN C 46 ALA C 107 ILE C 108 GLU C 110 SITE 3 AC3 16 LYS C 115 LEU C 118 ASN C 135 THR C 136 SITE 4 AC3 16 SER C 137 HIS C 158 PHE C 159 ASN C 161 CRYST1 227.200 82.100 124.700 90.00 90.00 90.00 C 2 2 21 24 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 0.004401 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012180 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008019 0.00000