HEADER LYASE 27-AUG-15 5DGD TITLE BENZOYLFORMATE DECARBOXYLASE F464I AND A460V MUTANT FROM PSEUDOMONAS TITLE 2 PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: BENZOYLFORMATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BFDC; COMPND 5 EC: 4.1.1.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 STRAIN: RF4738; SOURCE 5 GENE: MDLC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PREP7 KEYWDS BENZOYLFORMATE DECARBOXYLASE, THIAMIN DIPHOSPHATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,M.S.HASSON REVDAT 4 27-SEP-23 5DGD 1 REMARK REVDAT 3 04-AUG-21 5DGD 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 FORMUL LINK SITE ATOM REVDAT 2 30-SEP-15 5DGD 1 TITLE JRNL REVDAT 1 16-SEP-15 5DGD 0 JRNL AUTH A.K.BERA,M.S.HASSON JRNL TITL BENZOYLFORMATE DECARBOXYLASE F464I AND A460V MUTANT FROM JRNL TITL 2 PSEUDOMONAS PUTIDA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.K.BERA,L.S.POLOVNIKOVA,J.ROESTAMADJI,T.S.WIDLANSKI, REMARK 1 AUTH 2 G.L.KENYON,M.J.MCLEISH,M.S.HASSON REMARK 1 TITL MECHANISM-BASED INACTIVATION OF BENZOYLFORMATE REMARK 1 TITL 2 DECARBOXYLASE, A THIAMIN DIPHOSPHATE-DEPENDENT ENZYME. REMARK 1 REF J.AM.CHEM.SOC. V. 129 4120 2007 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 17367138 REMARK 1 DOI 10.1021/JA068636Z REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 192333 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 17.6541 - 2.7204 0.60 8737 91 0.1805 0.1776 REMARK 3 2 2.7204 - 2.1605 0.97 13824 145 0.1280 0.1385 REMARK 3 3 2.1605 - 1.8877 0.99 14091 149 0.1281 0.1417 REMARK 3 4 1.8877 - 1.7153 0.99 13922 145 0.1366 0.1274 REMARK 3 5 1.7153 - 1.5924 1.00 14008 147 0.1283 0.1381 REMARK 3 6 1.5924 - 1.4986 1.00 14029 148 0.1276 0.1297 REMARK 3 7 1.4986 - 1.4236 1.00 14025 147 0.1341 0.1475 REMARK 3 8 1.4236 - 1.3616 1.00 14010 147 0.1421 0.1611 REMARK 3 9 1.3616 - 1.3092 1.00 13955 147 0.1440 0.1724 REMARK 3 10 1.3092 - 1.2641 1.00 14054 148 0.1463 0.1449 REMARK 3 11 1.2641 - 1.2246 1.00 13874 144 0.1508 0.1856 REMARK 3 12 1.2246 - 1.1896 1.00 13971 147 0.1532 0.1559 REMARK 3 13 1.1896 - 1.1583 1.00 13953 146 0.1569 0.1924 REMARK 3 14 1.1583 - 1.1300 1.00 13883 146 0.1615 0.1554 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.65 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 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 : 0.011 4071 REMARK 3 ANGLE : 1.470 5566 REMARK 3 CHIRALITY : 0.085 623 REMARK 3 PLANARITY : 0.010 736 REMARK 3 DIHEDRAL : 12.734 1472 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 84.4958 30.3110 157.3121 REMARK 3 T TENSOR REMARK 3 T11: 0.0841 T22: 0.0680 REMARK 3 T33: 0.0761 T12: 0.0021 REMARK 3 T13: -0.0020 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 0.2491 L22: 0.1592 REMARK 3 L33: 0.2244 L12: -0.0634 REMARK 3 L13: 0.0287 L23: 0.0216 REMARK 3 S TENSOR REMARK 3 S11: 0.0030 S12: -0.0270 S13: -0.0434 REMARK 3 S21: 0.0209 S22: 0.0082 S23: -0.0098 REMARK 3 S31: 0.0520 S32: 0.0213 S33: -0.0120 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5DGD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000213082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9002 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 192537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.32600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.800 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: 1BFD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (V/V) PEG 400, 0.15 M CACL2, 0.5% REMARK 280 (V/V) MPD, 0.1 M TRISCL (PH 8.5), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 -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 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 1.000000 0.000000 0.000000 40.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.82800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.67250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.82800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.67250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.75000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.82800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.67250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.75000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.82800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.67250 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 27190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -278.0 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 -1.000000 0.000000 0.000000 163.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 95.65600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 163.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 274.69000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 95.65600 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 274.69000 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 MG MG A 603 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 905 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 984 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 987 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1229 LIES ON A SPECIAL POSITION. 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 HOH A 1051 O HOH A 1098 1.23 REMARK 500 O HOH A 1006 O HOH A 1118 1.56 REMARK 500 O HOH A 1028 O HOH A 1118 1.58 REMARK 500 O HOH A 907 O HOH A 1191 1.64 REMARK 500 O HOH A 1047 O HOH A 1071 1.69 REMARK 500 O HOH A 1191 O HOH A 1222 1.76 REMARK 500 O HOH A 705 O HOH A 965 1.93 REMARK 500 O HOH A 759 O HOH A 1132 1.97 REMARK 500 O HOH A 742 O HOH A 1188 1.98 REMARK 500 O HOH A 703 O HOH A 705 2.01 REMARK 500 O HOH A 1039 O HOH A 1094 2.02 REMARK 500 O HOH A 927 O HOH A 1060 2.07 REMARK 500 O HOH A 1133 O HOH A 1185 2.09 REMARK 500 O HOH A 1112 O HOH A 1130 2.10 REMARK 500 O HOH A 946 O HOH A 1126 2.12 REMARK 500 O HOH A 864 O HOH A 1231 2.15 REMARK 500 O HOH A 702 O HOH A 995 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 O HOH A 1047 O HOH A 1147 8557 1.86 REMARK 500 O HOH A 1234 O HOH A 1242 2765 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 103 CG MET A 103 SD -0.296 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 MET A 103 CG - SD - CE ANGL. DEV. = -17.6 DEGREES REMARK 500 ARG A 245 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 71 -148.40 48.64 REMARK 500 LEU A 110 4.60 81.22 REMARK 500 ASN A 202 64.37 -151.51 REMARK 500 HIS A 281 -75.82 -140.95 REMARK 500 ASP A 284 65.20 -154.41 REMARK 500 GLU A 375 47.68 -141.09 REMARK 500 PRO A 447 46.00 -85.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1247 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A1248 DISTANCE = 6.16 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 605 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 O REMARK 620 2 ASP A 364 OD1 122.9 REMARK 620 3 HOH A 713 O 121.5 3.0 REMARK 620 4 HOH A 800 O 119.2 3.7 3.8 REMARK 620 5 HOH A1203 O 122.3 4.0 6.7 4.9 REMARK 620 6 HOH A1235 O 121.8 1.6 3.9 2.8 2.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 117 O REMARK 620 2 ASN A 117 O 0.0 REMARK 620 3 LEU A 118 O 74.8 74.8 REMARK 620 4 LEU A 118 O 74.8 74.8 0.0 REMARK 620 5 ARG A 120 O 93.3 93.3 91.8 91.8 REMARK 620 6 ARG A 120 O 93.3 93.3 91.8 91.8 0.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 133 O REMARK 620 2 SER A 171 OG 108.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 606 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 347 OD1 REMARK 620 2 ASP A 347 OD2 50.7 REMARK 620 3 ALA A 416 O 35.5 74.4 REMARK 620 4 HOH A 919 O 33.6 72.3 2.2 REMARK 620 5 HOH A1012 O 37.4 74.6 2.6 3.8 REMARK 620 6 HOH A1031 O 36.6 77.6 3.8 5.5 5.6 REMARK 620 7 HOH A1115 O 39.2 77.7 3.7 5.9 3.2 3.9 REMARK 620 8 HOH A1147 O 33.5 74.6 3.3 3.6 5.9 3.3 6.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 604 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 428 OD1 REMARK 620 2 ASN A 455 OD1 87.2 REMARK 620 3 THR A 457 O 105.7 85.7 REMARK 620 4 TPP A 607 O2A 89.6 176.1 92.9 REMARK 620 5 TPP A 607 O3B 165.5 100.7 87.2 82.9 REMARK 620 6 HOH A 740 O 80.1 86.5 170.0 95.3 88.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TPP A 607 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DEI RELATED DB: PDB REMARK 900 RELATED ID: 5DGT RELATED DB: PDB DBREF 5DGD A 2 525 UNP P20906 MDLC_PSEPU 2 525 SEQADV 5DGD VAL A 460 UNP P20906 ALA 460 ENGINEERED MUTATION SEQADV 5DGD ILE A 464 UNP P20906 PHE 464 ENGINEERED MUTATION SEQRES 1 A 524 ALA SER VAL HIS GLY THR THR TYR GLU LEU LEU ARG ARG SEQRES 2 A 524 GLN GLY ILE ASP THR VAL PHE GLY ASN PRO GLY SER ASN SEQRES 3 A 524 GLU LEU PRO PHE LEU LYS ASP PHE PRO GLU ASP PHE ARG SEQRES 4 A 524 TYR ILE LEU ALA LEU GLN GLU ALA CYS VAL VAL GLY ILE SEQRES 5 A 524 ALA ASP GLY TYR ALA GLN ALA SER ARG LYS PRO ALA PHE SEQRES 6 A 524 ILE ASN LEU HIS SER ALA ALA GLY THR GLY ASN ALA MET SEQRES 7 A 524 GLY ALA LEU SER ASN ALA TRP ASN SER HIS SER PRO LEU SEQRES 8 A 524 ILE VAL THR ALA GLY GLN GLN THR ARG ALA MET ILE GLY SEQRES 9 A 524 VAL GLU ALA LEU LEU THR ASN VAL ASP ALA ALA ASN LEU SEQRES 10 A 524 PRO ARG PRO LEU VAL LYS TRP SER TYR GLU PRO ALA SER SEQRES 11 A 524 ALA ALA GLU VAL PRO HIS ALA MET SER ARG ALA ILE HIS SEQRES 12 A 524 MET ALA SER MET ALA PRO GLN GLY PRO VAL TYR LEU SER SEQRES 13 A 524 VAL PRO TYR ASP ASP TRP ASP LYS ASP ALA ASP PRO GLN SEQRES 14 A 524 SER HIS HIS LEU PHE ASP ARG HIS VAL SER SER SER VAL SEQRES 15 A 524 ARG LEU ASN ASP GLN ASP LEU ASP ILE LEU VAL LYS ALA SEQRES 16 A 524 LEU ASN SER ALA SER ASN PRO ALA ILE VAL LEU GLY PRO SEQRES 17 A 524 ASP VAL ASP ALA ALA ASN ALA ASN ALA ASP CYS VAL MET SEQRES 18 A 524 LEU ALA GLU ARG LEU LYS ALA PRO VAL TRP VAL ALA PRO SEQRES 19 A 524 SER ALA PRO ARG CYS PRO PHE PRO THR ARG HIS PRO CYS SEQRES 20 A 524 PHE ARG GLY LEU MET PRO ALA GLY ILE ALA ALA ILE SER SEQRES 21 A 524 GLN LEU LEU GLU GLY HIS ASP VAL VAL LEU VAL ILE GLY SEQRES 22 A 524 ALA PRO VAL PHE ARG TYR HIS GLN TYR ASP PRO GLY GLN SEQRES 23 A 524 TYR LEU LYS PRO GLY THR ARG LEU ILE SER VAL THR CYS SEQRES 24 A 524 ASP PRO LEU GLU ALA ALA ARG ALA PRO MET GLY ASP ALA SEQRES 25 A 524 ILE VAL ALA ASP ILE GLY ALA MET ALA SER ALA LEU ALA SEQRES 26 A 524 ASN LEU VAL GLU GLU SER SER ARG GLN LEU PRO THR ALA SEQRES 27 A 524 ALA PRO GLU PRO ALA LYS VAL ASP GLN ASP ALA GLY ARG SEQRES 28 A 524 LEU HIS PRO GLU THR VAL PHE ASP THR LEU ASN ASP MET SEQRES 29 A 524 ALA PRO GLU ASN ALA ILE TYR LEU ASN GLU SER THR SER SEQRES 30 A 524 THR THR ALA GLN MET TRP GLN ARG LEU ASN MET ARG ASN SEQRES 31 A 524 PRO GLY SER TYR TYR PHE CYS ALA ALA GLY GLY LEU GLY SEQRES 32 A 524 PHE ALA LEU PRO ALA ALA ILE GLY VAL GLN LEU ALA GLU SEQRES 33 A 524 PRO GLU ARG GLN VAL ILE ALA VAL ILE GLY ASP GLY SER SEQRES 34 A 524 ALA ASN TYR SER ILE SER ALA LEU TRP THR ALA ALA GLN SEQRES 35 A 524 TYR ASN ILE PRO THR ILE PHE VAL ILE MET ASN ASN GLY SEQRES 36 A 524 THR TYR GLY VAL LEU ARG TRP ILE ALA GLY VAL LEU GLU SEQRES 37 A 524 ALA GLU ASN VAL PRO GLY LEU ASP VAL PRO GLY ILE ASP SEQRES 38 A 524 PHE ARG ALA LEU ALA LYS GLY TYR GLY VAL GLN ALA LEU SEQRES 39 A 524 LYS ALA ASP ASN LEU GLU GLN LEU LYS GLY SER LEU GLN SEQRES 40 A 524 GLU ALA LEU SER ALA LYS GLY PRO VAL LEU ILE GLU VAL SEQRES 41 A 524 SER THR VAL SER HET MG A 601 1 HET MG A 602 1 HET MG A 603 1 HET CA A 604 1 HET CA A 605 1 HET CA A 606 1 HET TPP A 607 42 HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM TPP THIAMINE DIPHOSPHATE FORMUL 2 MG 3(MG 2+) FORMUL 5 CA 3(CA 2+) FORMUL 8 TPP C12 H19 N4 O7 P2 S 1+ FORMUL 9 HOH *548(H2 O) HELIX 1 AA1 SER A 3 GLN A 15 1 13 HELIX 2 AA2 GLY A 25 ASN A 27 5 3 HELIX 3 AA3 GLU A 28 LYS A 33 1 6 HELIX 4 AA4 GLN A 46 ARG A 62 1 17 HELIX 5 AA5 SER A 71 ALA A 78 1 8 HELIX 6 AA6 ALA A 78 SER A 88 1 11 HELIX 7 AA7 THR A 100 GLY A 105 1 6 HELIX 8 AA8 ASP A 114 LEU A 118 5 5 HELIX 9 AA9 SER A 131 ALA A 133 5 3 HELIX 10 AB1 GLU A 134 MET A 148 1 15 HELIX 11 AB2 ASP A 161 TRP A 163 5 3 HELIX 12 AB3 ASP A 168 PHE A 175 5 8 HELIX 13 AB4 ASN A 186 ALA A 200 1 15 HELIX 14 AB5 GLY A 208 ALA A 214 1 7 HELIX 15 AB6 ALA A 216 LYS A 228 1 13 HELIX 16 AB7 GLY A 256 GLU A 265 1 10 HELIX 17 AB8 ASP A 301 ALA A 308 1 8 HELIX 18 AB9 ASP A 317 VAL A 329 1 13 HELIX 19 AC1 HIS A 354 ALA A 366 1 13 HELIX 20 AC2 THR A 379 LEU A 387 1 9 HELIX 21 AC3 PHE A 405 GLU A 417 1 13 HELIX 22 AC4 GLY A 429 TYR A 433 5 5 HELIX 23 AC5 SER A 434 SER A 436 5 3 HELIX 24 AC6 ALA A 437 ASN A 445 1 9 HELIX 25 AC7 TYR A 458 GLU A 469 1 12 HELIX 26 AC8 ASP A 482 GLY A 491 1 10 HELIX 27 AC9 ASN A 499 SER A 512 1 14 SHEET 1 AA1 6 ARG A 40 LEU A 43 0 SHEET 2 AA1 6 THR A 19 GLY A 22 1 N VAL A 20 O ILE A 42 SHEET 3 AA1 6 ALA A 65 HIS A 70 1 O PHE A 66 N PHE A 21 SHEET 4 AA1 6 LEU A 92 GLN A 98 1 O ILE A 93 N ILE A 67 SHEET 5 AA1 6 VAL A 154 PRO A 159 1 O VAL A 154 N VAL A 94 SHEET 6 AA1 6 SER A 126 TYR A 127 1 N TYR A 127 O SER A 157 SHEET 1 AA2 6 PHE A 249 LEU A 252 0 SHEET 2 AA2 6 VAL A 231 VAL A 233 1 N VAL A 231 O ARG A 250 SHEET 3 AA2 6 ALA A 204 LEU A 207 1 N LEU A 207 O TRP A 232 SHEET 4 AA2 6 VAL A 269 ILE A 273 1 O ILE A 273 N VAL A 206 SHEET 5 AA2 6 ARG A 294 THR A 299 1 O ILE A 296 N VAL A 272 SHEET 6 AA2 6 ASP A 312 VAL A 315 1 O ILE A 314 N THR A 299 SHEET 1 AA3 6 TYR A 395 PHE A 397 0 SHEET 2 AA3 6 ILE A 371 GLU A 375 1 N ASN A 374 O TYR A 396 SHEET 3 AA3 6 VAL A 422 GLY A 427 1 O VAL A 425 N GLU A 375 SHEET 4 AA3 6 ILE A 449 ASN A 454 1 O VAL A 451 N ALA A 424 SHEET 5 AA3 6 VAL A 517 SER A 522 1 O VAL A 521 N ILE A 452 SHEET 6 AA3 6 GLN A 493 ALA A 497 1 N GLN A 493 O LEU A 518 LINK O GLU A 37 CA CA A 605 1555 8457 2.34 LINK O ASN A 117 MG MG A 603 1555 1555 2.66 LINK O ASN A 117 MG MG A 603 1555 2765 2.67 LINK O LEU A 118 MG MG A 603 1555 1555 2.49 LINK O LEU A 118 MG MG A 603 1555 2765 2.49 LINK O ARG A 120 MG MG A 603 1555 1555 2.47 LINK O ARG A 120 MG MG A 603 1555 2765 2.46 LINK O ALA A 133 MG MG A 601 1555 1555 2.73 LINK OG SER A 171 MG MG A 601 1555 1555 2.84 LINK OD1 ASP A 347 CA CA A 606 1555 8557 2.66 LINK OD2 ASP A 347 CA CA A 606 1555 8557 2.41 LINK OD1 ASP A 364 CA CA A 605 1555 1555 2.51 LINK O ALA A 416 CA CA A 606 1555 1555 2.32 LINK OD1 ASP A 428 CA CA A 604 1555 1555 2.30 LINK OD1 ASN A 455 CA CA A 604 1555 1555 2.30 LINK O THR A 457 CA CA A 604 1555 1555 2.29 LINK CA CA A 604 O2A TPP A 607 1555 1555 2.25 LINK CA CA A 604 O3B TPP A 607 1555 1555 2.32 LINK CA CA A 604 O HOH A 740 1555 1555 2.31 LINK CA CA A 605 O HOH A 713 1555 1555 2.62 LINK CA CA A 605 O HOH A 800 1555 1555 2.50 LINK CA CA A 605 O HOH A1203 1555 1555 2.82 LINK CA CA A 605 O HOH A1235 1555 1555 2.57 LINK CA CA A 606 O HOH A 919 1555 1555 2.47 LINK CA CA A 606 O HOH A1012 1555 1555 2.47 LINK CA CA A 606 O HOH A1031 1555 1555 2.60 LINK CA CA A 606 O HOH A1115 1555 1555 2.44 LINK CA CA A 606 O HOH A1147 1555 1555 2.46 CISPEP 1 ARG A 120 PRO A 121 0 11.19 CISPEP 2 ALA A 149 PRO A 150 0 -8.67 CISPEP 3 VAL A 277 PHE A 278 0 -20.88 SITE 1 AC1 5 ALA A 133 PRO A 136 ALA A 167 ASP A 168 SITE 2 AC1 5 SER A 171 SITE 1 AC2 2 ARG A 184 ASP A 187 SITE 1 AC3 4 ASN A 117 LEU A 118 ARG A 120 HOH A 984 SITE 1 AC4 5 ASP A 428 ASN A 455 THR A 457 TPP A 607 SITE 2 AC4 5 HOH A 740 SITE 1 AC5 6 GLU A 37 ASP A 364 HOH A 713 HOH A 800 SITE 2 AC5 6 HOH A1203 HOH A1235 SITE 1 AC6 7 ASP A 347 ALA A 416 HOH A 919 HOH A1012 SITE 2 AC6 7 HOH A1031 HOH A1115 HOH A1147 SITE 1 AC7 23 ASN A 23 PRO A 24 GLY A 25 GLU A 47 SITE 2 AC7 23 HIS A 70 ASN A 77 THR A 377 SER A 378 SITE 3 AC7 23 GLY A 401 LEU A 403 GLY A 427 ASP A 428 SITE 4 AC7 23 GLY A 429 SER A 430 TYR A 433 ASN A 455 SITE 5 AC7 23 THR A 457 TYR A 458 GLY A 459 VAL A 460 SITE 6 AC7 23 CA A 604 HOH A 751 HOH A 967 CRYST1 81.500 95.656 137.345 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007281 0.00000