HEADER OXIDOREDUCTASE 25-FEB-13 4JDR TITLE DIHYDROLIPOAMIDE DEHYDROGENASE OF PYRUVATE DEHYDROGENASE FROM TITLE 2 ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROLIPOYL DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DIHYDROLIPOAMIDE DEHYDROGENASE, E3 COMPONENT OF PYRUVATE AND COMPND 5 2-OXOGLUTARATE DEHYDROGENASES COMPLEXES, GLYCINE CLEAVAGE SYSTEM L COMPND 6 PROTEIN; COMPND 7 EC: 1.8.1.4; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: LPDA, LPD, B0116, JW0112; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPOAMIDE DEHYDROGENASE (E3); PYRUVATE DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.CHANDRASEKHAR,P.ARJUNAN,W.FUREY REVDAT 3 20-SEP-23 4JDR 1 REMARK REVDAT 2 12-JUN-13 4JDR 1 JRNL REVDAT 1 24-APR-13 4JDR 0 JRNL AUTH K.CHANDRASEKHAR,J.WANG,P.ARJUNAN,M.SAX,Y.H.PARK,N.S.NEMERIA, JRNL AUTH 2 S.KUMARAN,J.SONG,F.JORDAN,W.FUREY JRNL TITL INSIGHT TO THE INTERACTION OF THE DIHYDROLIPOAMIDE JRNL TITL 2 ACETYLTRANSFERASE (E2) CORE WITH THE PERIPHERAL COMPONENTS JRNL TITL 3 IN THE ESCHERICHIA COLI PYRUVATE DEHYDROGENASE COMPLEX VIA JRNL TITL 4 MULTIFACETED STRUCTURAL APPROACHES. JRNL REF J.BIOL.CHEM. V. 288 15402 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23580650 JRNL DOI 10.1074/JBC.M113.466789 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 52714 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.5500 - 2.5000 0.88 0 131 0.4110 0.4160 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 65.28 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.92990 REMARK 3 B22 (A**2) : -10.92990 REMARK 3 B33 (A**2) : 21.85980 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 7384 REMARK 3 ANGLE : 1.281 10020 REMARK 3 CHIRALITY : 0.075 1145 REMARK 3 PLANARITY : 0.006 1271 REMARK 3 DIHEDRAL : 16.958 2701 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 38.3541 0.1387 55.0657 REMARK 3 T TENSOR REMARK 3 T11: 0.3628 T22: 0.2763 REMARK 3 T33: 0.2737 T12: 0.0476 REMARK 3 T13: 0.0668 T23: -0.0340 REMARK 3 L TENSOR REMARK 3 L11: 0.8317 L22: 0.6022 REMARK 3 L33: 0.2442 L12: -0.6263 REMARK 3 L13: -0.3153 L23: 0.1192 REMARK 3 S TENSOR REMARK 3 S11: 0.2312 S12: 0.0443 S13: 0.1567 REMARK 3 S21: -0.2240 S22: -0.0925 S23: -0.1315 REMARK 3 S31: -0.0657 S32: -0.0157 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 68.3844 -8.1740 72.4769 REMARK 3 T TENSOR REMARK 3 T11: 0.2433 T22: 0.4507 REMARK 3 T33: 0.4086 T12: -0.0179 REMARK 3 T13: 0.0667 T23: -0.2015 REMARK 3 L TENSOR REMARK 3 L11: 0.4576 L22: 0.4221 REMARK 3 L33: 0.6948 L12: -0.4811 REMARK 3 L13: -0.0158 L23: 0.0068 REMARK 3 S TENSOR REMARK 3 S11: 0.0683 S12: -0.1642 S13: 0.4578 REMARK 3 S21: -0.0884 S22: 0.1450 S23: -0.2565 REMARK 3 S31: -0.0774 S32: 0.2423 S33: 0.0007 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 2:472 OR RESSEQ REMARK 3 600:600 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 2:472 OR RESSEQ REMARK 3 600:600 ) REMARK 3 ATOM PAIRS NUMBER : 3591 REMARK 3 RMSD : 0.219 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000077918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 93.0 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : DOUBLE CRYSTAL SI(111) SAGITTAL REMARK 200 FOCUSING; VERTICAL FOCUSING REMARK 200 MIRROR. REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54508 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 35.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 7.480 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.76 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 1OJT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMMONIUM SULFATE, 0.1M MES, PH REMARK 280 6.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 90.00000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 90.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 98.45000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 90.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 90.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 98.45000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 90.00000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 90.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 98.45000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 90.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 90.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 98.45000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 90.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 90.00000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 98.45000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 90.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 90.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 98.45000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 90.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 90.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 98.45000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 90.00000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 90.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 98.45000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 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 1 REMARK 465 LYS A 473 REMARK 465 LYS A 474 REMARK 465 MET B 1 REMARK 465 LYS B 473 REMARK 465 LYS B 474 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 VAL A 48 30.20 -142.85 REMARK 500 THR A 120 -73.25 -77.60 REMARK 500 ASN A 123 13.97 -145.57 REMARK 500 ALA A 144 56.09 -140.78 REMARK 500 ALA A 270 65.34 -118.77 REMARK 500 ASN A 276 31.14 -94.24 REMARK 500 THR A 303 -178.59 -66.40 REMARK 500 PRO A 306 -37.81 -35.61 REMARK 500 TYR A 352 41.97 -91.93 REMARK 500 CYS A 392 42.96 -151.42 REMARK 500 ASN A 417 19.84 54.31 REMARK 500 VAL B 48 29.06 -146.49 REMARK 500 THR B 120 -73.01 -79.93 REMARK 500 ALA B 122 0.94 -68.51 REMARK 500 ASN B 123 14.48 -147.11 REMARK 500 GLU B 130 -53.62 -29.37 REMARK 500 ALA B 144 56.29 -142.85 REMARK 500 PHE B 207 172.65 -58.07 REMARK 500 ALA B 270 66.04 -119.75 REMARK 500 LYS B 284 7.53 -69.31 REMARK 500 THR B 303 -178.39 -68.24 REMARK 500 PRO B 306 -37.23 -36.15 REMARK 500 ILE B 314 7.59 -67.08 REMARK 500 TYR B 352 44.52 -90.82 REMARK 500 CYS B 392 46.23 -146.95 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 FAD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 504 DBREF 4JDR A 1 474 UNP P0A9P0 DLDH_ECOLI 1 474 DBREF 4JDR B 1 474 UNP P0A9P0 DLDH_ECOLI 1 474 SEQRES 1 A 474 MET SER THR GLU ILE LYS THR GLN VAL VAL VAL LEU GLY SEQRES 2 A 474 ALA GLY PRO ALA GLY TYR SER ALA ALA PHE ARG CYS ALA SEQRES 3 A 474 ASP LEU GLY LEU GLU THR VAL ILE VAL GLU ARG TYR ASN SEQRES 4 A 474 THR LEU GLY GLY VAL CYS LEU ASN VAL GLY CYS ILE PRO SEQRES 5 A 474 SER LYS ALA LEU LEU HIS VAL ALA LYS VAL ILE GLU GLU SEQRES 6 A 474 ALA LYS ALA LEU ALA GLU HIS GLY ILE VAL PHE GLY GLU SEQRES 7 A 474 PRO LYS THR ASP ILE ASP LYS ILE ARG THR TRP LYS GLU SEQRES 8 A 474 LYS VAL ILE ASN GLN LEU THR GLY GLY LEU ALA GLY MET SEQRES 9 A 474 ALA LYS GLY ARG LYS VAL LYS VAL VAL ASN GLY LEU GLY SEQRES 10 A 474 LYS PHE THR GLY ALA ASN THR LEU GLU VAL GLU GLY GLU SEQRES 11 A 474 ASN GLY LYS THR VAL ILE ASN PHE ASP ASN ALA ILE ILE SEQRES 12 A 474 ALA ALA GLY SER ARG PRO ILE GLN LEU PRO PHE ILE PRO SEQRES 13 A 474 HIS GLU ASP PRO ARG ILE TRP ASP SER THR ASP ALA LEU SEQRES 14 A 474 GLU LEU LYS GLU VAL PRO GLU ARG LEU LEU VAL MET GLY SEQRES 15 A 474 GLY GLY ILE ILE GLY LEU GLU MET GLY THR VAL TYR HIS SEQRES 16 A 474 ALA LEU GLY SER GLN ILE ASP VAL VAL GLU MET PHE ASP SEQRES 17 A 474 GLN VAL ILE PRO ALA ALA ASP LYS ASP ILE VAL LYS VAL SEQRES 18 A 474 PHE THR LYS ARG ILE SER LYS LYS PHE ASN LEU MET LEU SEQRES 19 A 474 GLU THR LYS VAL THR ALA VAL GLU ALA LYS GLU ASP GLY SEQRES 20 A 474 ILE TYR VAL THR MET GLU GLY LYS LYS ALA PRO ALA GLU SEQRES 21 A 474 PRO GLN ARG TYR ASP ALA VAL LEU VAL ALA ILE GLY ARG SEQRES 22 A 474 VAL PRO ASN GLY LYS ASN LEU ASP ALA GLY LYS ALA GLY SEQRES 23 A 474 VAL GLU VAL ASP ASP ARG GLY PHE ILE ARG VAL ASP LYS SEQRES 24 A 474 GLN LEU ARG THR ASN VAL PRO HIS ILE PHE ALA ILE GLY SEQRES 25 A 474 ASP ILE VAL GLY GLN PRO MET LEU ALA HIS LYS GLY VAL SEQRES 26 A 474 HIS GLU GLY HIS VAL ALA ALA GLU VAL ILE ALA GLY LYS SEQRES 27 A 474 LYS HIS TYR PHE ASP PRO LYS VAL ILE PRO SER ILE ALA SEQRES 28 A 474 TYR THR GLU PRO GLU VAL ALA TRP VAL GLY LEU THR GLU SEQRES 29 A 474 LYS GLU ALA LYS GLU LYS GLY ILE SER TYR GLU THR ALA SEQRES 30 A 474 THR PHE PRO TRP ALA ALA SER GLY ARG ALA ILE ALA SER SEQRES 31 A 474 ASP CYS ALA ASP GLY MET THR LYS LEU ILE PHE ASP LYS SEQRES 32 A 474 GLU SER HIS ARG VAL ILE GLY GLY ALA ILE VAL GLY THR SEQRES 33 A 474 ASN GLY GLY GLU LEU LEU GLY GLU ILE GLY LEU ALA ILE SEQRES 34 A 474 GLU MET GLY CYS ASP ALA GLU ASP ILE ALA LEU THR ILE SEQRES 35 A 474 HIS ALA HIS PRO THR LEU HIS GLU SER VAL GLY LEU ALA SEQRES 36 A 474 ALA GLU VAL PHE GLU GLY SER ILE THR ASP LEU PRO ASN SEQRES 37 A 474 PRO LYS ALA LYS LYS LYS SEQRES 1 B 474 MET SER THR GLU ILE LYS THR GLN VAL VAL VAL LEU GLY SEQRES 2 B 474 ALA GLY PRO ALA GLY TYR SER ALA ALA PHE ARG CYS ALA SEQRES 3 B 474 ASP LEU GLY LEU GLU THR VAL ILE VAL GLU ARG TYR ASN SEQRES 4 B 474 THR LEU GLY GLY VAL CYS LEU ASN VAL GLY CYS ILE PRO SEQRES 5 B 474 SER LYS ALA LEU LEU HIS VAL ALA LYS VAL ILE GLU GLU SEQRES 6 B 474 ALA LYS ALA LEU ALA GLU HIS GLY ILE VAL PHE GLY GLU SEQRES 7 B 474 PRO LYS THR ASP ILE ASP LYS ILE ARG THR TRP LYS GLU SEQRES 8 B 474 LYS VAL ILE ASN GLN LEU THR GLY GLY LEU ALA GLY MET SEQRES 9 B 474 ALA LYS GLY ARG LYS VAL LYS VAL VAL ASN GLY LEU GLY SEQRES 10 B 474 LYS PHE THR GLY ALA ASN THR LEU GLU VAL GLU GLY GLU SEQRES 11 B 474 ASN GLY LYS THR VAL ILE ASN PHE ASP ASN ALA ILE ILE SEQRES 12 B 474 ALA ALA GLY SER ARG PRO ILE GLN LEU PRO PHE ILE PRO SEQRES 13 B 474 HIS GLU ASP PRO ARG ILE TRP ASP SER THR ASP ALA LEU SEQRES 14 B 474 GLU LEU LYS GLU VAL PRO GLU ARG LEU LEU VAL MET GLY SEQRES 15 B 474 GLY GLY ILE ILE GLY LEU GLU MET GLY THR VAL TYR HIS SEQRES 16 B 474 ALA LEU GLY SER GLN ILE ASP VAL VAL GLU MET PHE ASP SEQRES 17 B 474 GLN VAL ILE PRO ALA ALA ASP LYS ASP ILE VAL LYS VAL SEQRES 18 B 474 PHE THR LYS ARG ILE SER LYS LYS PHE ASN LEU MET LEU SEQRES 19 B 474 GLU THR LYS VAL THR ALA VAL GLU ALA LYS GLU ASP GLY SEQRES 20 B 474 ILE TYR VAL THR MET GLU GLY LYS LYS ALA PRO ALA GLU SEQRES 21 B 474 PRO GLN ARG TYR ASP ALA VAL LEU VAL ALA ILE GLY ARG SEQRES 22 B 474 VAL PRO ASN GLY LYS ASN LEU ASP ALA GLY LYS ALA GLY SEQRES 23 B 474 VAL GLU VAL ASP ASP ARG GLY PHE ILE ARG VAL ASP LYS SEQRES 24 B 474 GLN LEU ARG THR ASN VAL PRO HIS ILE PHE ALA ILE GLY SEQRES 25 B 474 ASP ILE VAL GLY GLN PRO MET LEU ALA HIS LYS GLY VAL SEQRES 26 B 474 HIS GLU GLY HIS VAL ALA ALA GLU VAL ILE ALA GLY LYS SEQRES 27 B 474 LYS HIS TYR PHE ASP PRO LYS VAL ILE PRO SER ILE ALA SEQRES 28 B 474 TYR THR GLU PRO GLU VAL ALA TRP VAL GLY LEU THR GLU SEQRES 29 B 474 LYS GLU ALA LYS GLU LYS GLY ILE SER TYR GLU THR ALA SEQRES 30 B 474 THR PHE PRO TRP ALA ALA SER GLY ARG ALA ILE ALA SER SEQRES 31 B 474 ASP CYS ALA ASP GLY MET THR LYS LEU ILE PHE ASP LYS SEQRES 32 B 474 GLU SER HIS ARG VAL ILE GLY GLY ALA ILE VAL GLY THR SEQRES 33 B 474 ASN GLY GLY GLU LEU LEU GLY GLU ILE GLY LEU ALA ILE SEQRES 34 B 474 GLU MET GLY CYS ASP ALA GLU ASP ILE ALA LEU THR ILE SEQRES 35 B 474 HIS ALA HIS PRO THR LEU HIS GLU SER VAL GLY LEU ALA SEQRES 36 B 474 ALA GLU VAL PHE GLU GLY SER ILE THR ASP LEU PRO ASN SEQRES 37 B 474 PRO LYS ALA LYS LYS LYS HET FAD A 501 53 HET MES A 502 12 HET MES A 503 12 HET SO4 A 504 5 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 A 508 5 HET FAD B 501 53 HET MES B 502 12 HET SO4 B 503 5 HET SO4 B 504 5 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM SO4 SULFATE ION FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 4 MES 3(C6 H13 N O4 S) FORMUL 6 SO4 7(O4 S 2-) FORMUL 15 HOH *417(H2 O) HELIX 1 1 GLY A 15 LEU A 28 1 14 HELIX 2 2 GLY A 42 VAL A 48 1 7 HELIX 3 3 GLY A 49 LEU A 69 1 21 HELIX 4 4 ALA A 70 HIS A 72 5 3 HELIX 5 5 ASP A 82 ARG A 108 1 27 HELIX 6 6 ASP A 164 GLU A 170 1 7 HELIX 7 7 GLY A 184 LEU A 197 1 14 HELIX 8 8 ASP A 215 SER A 227 1 13 HELIX 9 9 GLY A 277 LEU A 280 5 4 HELIX 10 10 ASP A 281 GLY A 286 5 6 HELIX 11 11 GLY A 312 GLY A 316 5 5 HELIX 12 12 LEU A 320 ALA A 336 1 17 HELIX 13 13 THR A 363 LYS A 370 1 8 HELIX 14 14 SER A 384 SER A 390 1 7 HELIX 15 15 ASN A 417 GLU A 420 5 4 HELIX 16 16 LEU A 421 MET A 431 1 11 HELIX 17 17 ASP A 434 THR A 441 1 8 HELIX 18 18 HIS A 449 GLU A 460 1 12 HELIX 19 19 GLY B 15 LEU B 28 1 14 HELIX 20 20 GLY B 42 VAL B 48 1 7 HELIX 21 21 GLY B 49 ALA B 70 1 22 HELIX 22 22 ASP B 82 ARG B 108 1 27 HELIX 23 23 ASP B 164 GLU B 170 1 7 HELIX 24 24 GLY B 184 LEU B 197 1 14 HELIX 25 25 ASP B 215 SER B 227 1 13 HELIX 26 26 GLY B 277 LEU B 280 5 4 HELIX 27 27 ASP B 281 GLY B 286 5 6 HELIX 28 28 GLY B 312 GLY B 316 5 5 HELIX 29 29 LEU B 320 ALA B 336 1 17 HELIX 30 30 THR B 363 LYS B 370 1 8 HELIX 31 31 SER B 384 SER B 390 1 7 HELIX 32 32 ASN B 417 GLU B 420 5 4 HELIX 33 33 LEU B 421 MET B 431 1 11 HELIX 34 34 ASP B 434 LEU B 440 1 7 HELIX 35 35 HIS B 449 GLU B 460 1 12 SHEET 1 A 6 LYS A 111 ASN A 114 0 SHEET 2 A 6 THR A 32 GLU A 36 1 N ILE A 34 O LYS A 111 SHEET 3 A 6 THR A 3 LEU A 12 1 N VAL A 11 O VAL A 35 SHEET 4 A 6 THR A 134 ILE A 143 1 O ASN A 140 N GLN A 8 SHEET 5 A 6 THR A 124 GLU A 128 -1 N LEU A 125 O ILE A 136 SHEET 6 A 6 LEU A 116 GLY A 121 -1 N LYS A 118 O GLU A 126 SHEET 1 B 5 LYS A 111 ASN A 114 0 SHEET 2 B 5 THR A 32 GLU A 36 1 N ILE A 34 O LYS A 111 SHEET 3 B 5 THR A 3 LEU A 12 1 N VAL A 11 O VAL A 35 SHEET 4 B 5 THR A 134 ILE A 143 1 O ASN A 140 N GLN A 8 SHEET 5 B 5 ILE A 308 ALA A 310 1 O PHE A 309 N ILE A 143 SHEET 1 C 2 ILE A 74 VAL A 75 0 SHEET 2 C 2 LYS B 80 THR B 81 -1 O LYS B 80 N VAL A 75 SHEET 1 D 2 LYS A 80 THR A 81 0 SHEET 2 D 2 ILE B 74 VAL B 75 -1 O VAL B 75 N LYS A 80 SHEET 1 E 2 SER A 147 PRO A 149 0 SHEET 2 E 2 ARG A 273 PRO A 275 -1 O VAL A 274 N ARG A 148 SHEET 1 F 5 ILE A 162 TRP A 163 0 SHEET 2 F 5 ALA A 266 VAL A 269 1 O VAL A 267 N TRP A 163 SHEET 3 F 5 ARG A 177 MET A 181 1 N LEU A 179 O LEU A 268 SHEET 4 F 5 GLN A 200 GLU A 205 1 O ASP A 202 N VAL A 180 SHEET 5 F 5 ASN A 231 LEU A 234 1 O ASN A 231 N VAL A 203 SHEET 1 G 3 THR A 236 LYS A 244 0 SHEET 2 G 3 GLY A 247 GLY A 254 -1 O TYR A 249 N GLU A 242 SHEET 3 G 3 GLN A 262 TYR A 264 -1 O TYR A 264 N ILE A 248 SHEET 1 H 5 SER A 349 ALA A 351 0 SHEET 2 H 5 GLU A 356 GLY A 361 -1 O VAL A 357 N ALA A 351 SHEET 3 H 5 VAL A 408 GLY A 415 -1 O ILE A 413 N ALA A 358 SHEET 4 H 5 MET A 396 ASP A 402 -1 N ILE A 400 O ILE A 409 SHEET 5 H 5 TYR A 374 PRO A 380 -1 N GLU A 375 O PHE A 401 SHEET 1 I 6 LYS B 111 ASN B 114 0 SHEET 2 I 6 THR B 32 GLU B 36 1 N ILE B 34 O LYS B 111 SHEET 3 I 6 THR B 3 LEU B 12 1 N VAL B 11 O VAL B 35 SHEET 4 I 6 THR B 134 ILE B 143 1 O ASN B 140 N GLN B 8 SHEET 5 I 6 THR B 124 GLU B 128 -1 N LEU B 125 O ILE B 136 SHEET 6 I 6 LEU B 116 GLY B 121 -1 N LYS B 118 O GLU B 126 SHEET 1 J 5 LYS B 111 ASN B 114 0 SHEET 2 J 5 THR B 32 GLU B 36 1 N ILE B 34 O LYS B 111 SHEET 3 J 5 THR B 3 LEU B 12 1 N VAL B 11 O VAL B 35 SHEET 4 J 5 THR B 134 ILE B 143 1 O ASN B 140 N GLN B 8 SHEET 5 J 5 ILE B 308 ALA B 310 1 O PHE B 309 N ILE B 143 SHEET 1 K 2 SER B 147 PRO B 149 0 SHEET 2 K 2 ARG B 273 PRO B 275 -1 O VAL B 274 N ARG B 148 SHEET 1 L 5 ILE B 162 TRP B 163 0 SHEET 2 L 5 ALA B 266 VAL B 269 1 O VAL B 267 N TRP B 163 SHEET 3 L 5 ARG B 177 MET B 181 1 N LEU B 179 O LEU B 268 SHEET 4 L 5 GLN B 200 GLU B 205 1 O ASP B 202 N VAL B 180 SHEET 5 L 5 ASN B 231 LEU B 234 1 O MET B 233 N VAL B 203 SHEET 1 M 3 THR B 236 LYS B 244 0 SHEET 2 M 3 GLY B 247 GLY B 254 -1 O TYR B 249 N GLU B 242 SHEET 3 M 3 GLN B 262 TYR B 264 -1 O GLN B 262 N VAL B 250 SHEET 1 N 5 SER B 349 ALA B 351 0 SHEET 2 N 5 GLU B 356 GLY B 361 -1 O VAL B 357 N ALA B 351 SHEET 3 N 5 VAL B 408 GLY B 415 -1 O ILE B 413 N ALA B 358 SHEET 4 N 5 MET B 396 ASP B 402 -1 N ILE B 400 O ILE B 409 SHEET 5 N 5 TYR B 374 PRO B 380 -1 N GLU B 375 O PHE B 401 SSBOND 1 CYS A 45 CYS A 50 1555 1555 1.96 SSBOND 2 CYS B 45 CYS B 50 1555 1555 2.04 CISPEP 1 GLN A 317 PRO A 318 0 -8.05 CISPEP 2 GLU A 354 PRO A 355 0 4.77 CISPEP 3 HIS A 445 PRO A 446 0 3.24 CISPEP 4 GLN B 317 PRO B 318 0 -6.16 CISPEP 5 GLU B 354 PRO B 355 0 1.12 CISPEP 6 HIS B 445 PRO B 446 0 3.60 SITE 1 AC1 40 GLY A 13 ALA A 14 GLY A 15 PRO A 16 SITE 2 AC1 40 ALA A 17 GLU A 36 ARG A 37 TYR A 38 SITE 3 AC1 40 GLY A 43 VAL A 44 CYS A 45 GLY A 49 SITE 4 AC1 40 CYS A 50 LYS A 54 GLY A 115 LEU A 116 SITE 5 AC1 40 GLY A 117 ALA A 144 ALA A 145 GLY A 146 SITE 6 AC1 40 ILE A 186 ARG A 273 LEU A 280 GLY A 312 SITE 7 AC1 40 ASP A 313 MET A 319 LEU A 320 ALA A 321 SITE 8 AC1 40 HIS A 322 TYR A 352 HOH A 601 HOH A 616 SITE 9 AC1 40 HOH A 639 HOH A 648 HOH A 649 HOH A 650 SITE 10 AC1 40 HOH A 779 HOH A 828 HIS B 445 HOH B 720 SITE 1 AC2 9 ILE A 185 ILE A 211 PRO A 212 ALA A 213 SITE 2 AC2 9 GLN A 317 PRO A 318 LEU A 320 MES A 503 SITE 3 AC2 9 SO4 A 504 SITE 1 AC3 9 GLY A 182 GLY A 184 VAL A 204 GLU A 205 SITE 2 AC3 9 MET A 206 ILE A 271 MES A 502 SO4 A 504 SITE 3 AC3 9 HOH A 690 SITE 1 AC4 6 ILE A 185 ILE A 186 MES A 502 MES A 503 SITE 2 AC4 6 HOH A 664 HOH A 690 SITE 1 AC5 3 ASP A 281 ALA A 282 GLY A 283 SITE 1 AC6 3 ARG A 263 HOH A 685 HOH A 731 SITE 1 AC7 2 ASP A 298 LYS A 299 SITE 1 AC8 3 TYR A 374 GLU A 375 THR A 376 SITE 1 AC9 40 HIS A 445 HOH A 711 GLY B 13 ALA B 14 SITE 2 AC9 40 GLY B 15 PRO B 16 ALA B 17 GLU B 36 SITE 3 AC9 40 ARG B 37 TYR B 38 GLY B 43 VAL B 44 SITE 4 AC9 40 CYS B 45 GLY B 49 CYS B 50 LYS B 54 SITE 5 AC9 40 GLY B 115 LEU B 116 GLY B 117 ALA B 144 SITE 6 AC9 40 ALA B 145 GLY B 146 ILE B 186 ARG B 273 SITE 7 AC9 40 LEU B 280 GLY B 312 ASP B 313 MET B 319 SITE 8 AC9 40 LEU B 320 ALA B 321 HIS B 322 TYR B 352 SITE 9 AC9 40 HOH B 603 HOH B 614 HOH B 625 HOH B 643 SITE 10 AC9 40 HOH B 658 HOH B 714 HOH B 718 HOH B 760 SITE 1 BC1 9 GLY B 184 ILE B 185 ILE B 186 PRO B 212 SITE 2 BC1 9 ALA B 213 HOH B 666 HOH B 683 HOH B 734 SITE 3 BC1 9 HOH B 766 SITE 1 BC2 1 ARG B 263 SITE 1 BC3 4 GLY B 121 ALA B 122 ASN B 123 THR B 124 CRYST1 180.000 180.000 196.900 90.00 90.00 90.00 I 4 2 2 32 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 0.005556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005079 0.00000