HEADER LYASE 11-JAN-16 5HI0 TITLE THE SUBSTRATE BINDING MODE AND CHEMICAL BASIS OF A REACTION TITLE 2 SPECIFICITY SWITCH IN OXALATE DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXALATE DECARBOXYLASE OXDC; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.1.2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: OXDC, YVRK, BSU33240; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS OXIREDUCTASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR W.ZHU,L.M.EASTHON,L.A.REINHARDT,C.TU,S.E.COHEN,D.N.SILVERMAN, AUTHOR 2 K.N.ALLEN,N.G.J.RICHARDS REVDAT 6 27-SEP-23 5HI0 1 REMARK REVDAT 5 25-DEC-19 5HI0 1 REMARK REVDAT 4 20-NOV-19 5HI0 1 SEQRES LINK REVDAT 3 20-SEP-17 5HI0 1 JRNL REMARK REVDAT 2 27-APR-16 5HI0 1 JRNL REVDAT 1 06-APR-16 5HI0 0 JRNL AUTH W.ZHU,L.M.EASTHON,L.A.REINHARDT,C.TU,S.E.COHEN, JRNL AUTH 2 D.N.SILVERMAN,K.N.ALLEN,N.G.RICHARDS JRNL TITL SUBSTRATE BINDING MODE AND MOLECULAR BASIS OF A SPECIFICITY JRNL TITL 2 SWITCH IN OXALATE DECARBOXYLASE. JRNL REF BIOCHEMISTRY V. 55 2163 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27014926 JRNL DOI 10.1021/ACS.BIOCHEM.6B00043 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 17122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1712 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 10.0000 - 5.9330 1.00 1359 151 0.1742 0.1997 REMARK 3 2 5.9330 - 4.7199 1.00 1311 146 0.1635 0.1912 REMARK 3 3 4.7199 - 4.1264 1.00 1304 145 0.1393 0.1934 REMARK 3 4 4.1264 - 3.7505 1.00 1293 144 0.1542 0.1726 REMARK 3 5 3.7505 - 3.4825 1.00 1297 144 0.1657 0.2276 REMARK 3 6 3.4825 - 3.2776 1.00 1271 141 0.1726 0.2419 REMARK 3 7 3.2776 - 3.1138 1.00 1291 143 0.1797 0.2337 REMARK 3 8 3.1138 - 2.9785 1.00 1289 143 0.1794 0.2809 REMARK 3 9 2.9785 - 2.8640 1.00 1286 144 0.2203 0.2875 REMARK 3 10 2.8640 - 2.7653 1.00 1293 142 0.2146 0.2678 REMARK 3 11 2.7653 - 2.6789 0.99 1255 140 0.2467 0.3220 REMARK 3 12 2.6789 - 2.6025 0.90 1161 129 0.2548 0.3314 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 3079 REMARK 3 ANGLE : 1.105 4183 REMARK 3 CHIRALITY : 0.044 443 REMARK 3 PLANARITY : 0.005 551 REMARK 3 DIHEDRAL : 14.071 1126 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5HI0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17137 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 24.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 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: PHENIX 1.8.4_1496 REMARK 200 STARTING MODEL: 1UW8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CHES, PH 9.5, 10% PEG 6000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 77.30950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.63466 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 40.65133 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 77.30950 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 44.63466 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 40.65133 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 77.30950 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 44.63466 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 40.65133 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 77.30950 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 44.63466 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 40.65133 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 77.30950 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 44.63466 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 40.65133 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 77.30950 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 44.63466 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 40.65133 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 89.26932 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 81.30267 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 89.26932 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 81.30267 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 89.26932 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 81.30267 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 89.26932 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 81.30267 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 89.26932 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 81.30267 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 89.26932 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 81.30267 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 46610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 69770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -393.0 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 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 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 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 2 REMARK 465 LYS A 3 REMARK 465 GLN A 4 REMARK 465 ASN A 5 REMARK 465 CYS A 382 REMARK 465 SER A 383 REMARK 465 LYS A 384 REMARK 465 HIS A 385 REMARK 465 HIS A 386 REMARK 465 HIS A 387 REMARK 465 HIS A 388 REMARK 465 HIS A 389 REMARK 465 HIS A 390 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 GLU A 220 CG CD OE1 OE2 REMARK 470 GLU A 233 CG CD OE1 OE2 REMARK 470 LYS A 379 CD CE NZ REMARK 470 LYS A 381 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 CO CO A 402 O HOH A 503 1.55 REMARK 500 CO CO A 401 O2 OXL A 403 1.67 REMARK 500 O HOH A 501 O HOH A 515 1.79 REMARK 500 O HOH A 530 O HOH A 561 1.97 REMARK 500 O GLU A 72 O HOH A 501 1.99 REMARK 500 O HOH A 528 O HOH A 600 2.00 REMARK 500 O HOH A 590 O HOH A 594 2.05 REMARK 500 O HOH A 510 O HOH A 603 2.07 REMARK 500 OE1 GLU A 270 O HOH A 502 2.09 REMARK 500 O HOH A 591 O HOH A 596 2.10 REMARK 500 NE2 HIS A 272 O HOH A 503 2.11 REMARK 500 OD1 ASN A 47 O HOH A 504 2.13 REMARK 500 OE1 GLU A 93 O HOH A 505 2.14 REMARK 500 O HOH A 565 O HOH A 600 2.15 REMARK 500 O HOH A 503 O HOH A 524 2.16 REMARK 500 O HOH A 581 O HOH A 604 2.17 REMARK 500 O ASN A 162 OG1 THR A 164 2.19 REMARK 500 O GLU A 373 O HOH A 506 2.19 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 504 O HOH A 511 5555 2.02 REMARK 500 O HOH A 583 O HOH A 593 2555 2.15 REMARK 500 O HOH A 548 O HOH A 593 2555 2.17 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 ASN A 24 79.83 -105.36 REMARK 500 ASN A 31 64.98 -117.54 REMARK 500 LEU A 94 128.12 -37.27 REMARK 500 LEU A 145 -152.11 -88.44 REMARK 500 ASP A 156 49.01 -83.21 REMARK 500 PHE A 160 103.47 -48.27 REMARK 500 SER A 163 53.71 29.02 REMARK 500 TYR A 199 -71.11 73.33 REMARK 500 SER A 237 -168.37 -123.15 REMARK 500 SER A 295 173.07 69.46 REMARK 500 ALA A 315 -6.92 74.03 REMARK 500 REMARK 500 REMARK: NULL 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 CO A 401 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 NE2 REMARK 620 2 HIS A 97 NE2 95.4 REMARK 620 3 GLU A 101 OE1 156.2 105.4 REMARK 620 4 HIS A 140 NE2 85.0 123.9 92.7 REMARK 620 5 HOH A 516 O 86.5 153.5 69.8 82.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 402 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 272 NE2 REMARK 620 2 HIS A 274 NE2 91.7 REMARK 620 3 GLU A 279 OE1 169.8 86.0 REMARK 620 4 HIS A 318 NE2 84.0 125.2 105.5 REMARK 620 5 HOH A 524 O 93.5 145.5 82.9 89.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OXL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 DBREF 5HI0 A 1 384 UNP O34714 OXDC_BACSU 1 385 SEQADV 5HI0 A UNP O34714 GLU 162 DELETION SEQADV 5HI0 HIS A 385 UNP O34714 EXPRESSION TAG SEQADV 5HI0 HIS A 386 UNP O34714 EXPRESSION TAG SEQADV 5HI0 HIS A 387 UNP O34714 EXPRESSION TAG SEQADV 5HI0 HIS A 388 UNP O34714 EXPRESSION TAG SEQADV 5HI0 HIS A 389 UNP O34714 EXPRESSION TAG SEQADV 5HI0 HIS A 390 UNP O34714 EXPRESSION TAG SEQRES 1 A 390 MET LYS LYS GLN ASN ASP ILE PRO GLN PRO ILE ARG GLY SEQRES 2 A 390 ASP LYS GLY ALA THR VAL LYS ILE PRO ARG ASN ILE GLU SEQRES 3 A 390 ARG ASP ARG GLN ASN PRO ASP MET LEU VAL PRO PRO GLU SEQRES 4 A 390 THR ASP HIS GLY THR VAL SER ASN MET LYS PHE SER PHE SEQRES 5 A 390 SER ASP THR HIS ASN ARG LEU GLU LYS GLY GLY TYR ALA SEQRES 6 A 390 ARG GLU VAL THR VAL ARG GLU LEU PRO ILE SER GLU ASN SEQRES 7 A 390 LEU ALA SER VAL ASN MET ARG LEU LYS PRO GLY ALA ILE SEQRES 8 A 390 ARG GLU LEU HIS TRP HIS LYS GLU ALA GLU TRP ALA TYR SEQRES 9 A 390 MET ILE TYR GLY SER ALA ARG VAL THR ILE VAL ASP GLU SEQRES 10 A 390 LYS GLY ARG SER PHE ILE ASP ASP VAL GLY GLU GLY ASP SEQRES 11 A 390 LEU TRP TYR PHE PRO SER GLY LEU PRO HIS SER ILE GLN SEQRES 12 A 390 ALA LEU GLU GLU GLY ALA GLU PHE LEU LEU VAL PHE ASP SEQRES 13 A 390 ASP GLY SER PHE SER ASN SER THR PHE GLN LEU THR ASP SEQRES 14 A 390 TRP LEU ALA HIS THR PRO LYS GLU VAL ILE ALA ALA ASN SEQRES 15 A 390 PHE GLY VAL THR LYS GLU GLU ILE SER ASN LEU PRO GLY SEQRES 16 A 390 LYS GLU LYS TYR ILE PHE GLU ASN GLN LEU PRO GLY SER SEQRES 17 A 390 LEU LYS ASP ASP ILE VAL GLU GLY PRO ASN GLY GLU VAL SEQRES 18 A 390 PRO TYR PRO PHE THR TYR ARG LEU LEU GLU GLN GLU PRO SEQRES 19 A 390 ILE GLU SER GLU GLY GLY LYS VAL TYR ILE ALA ASP SER SEQRES 20 A 390 THR ASN PHE LYS VAL SER LYS THR ILE ALA SER ALA LEU SEQRES 21 A 390 VAL THR VAL GLU PRO GLY ALA MET ARG GLU LEU HIS TRP SEQRES 22 A 390 HIS PRO ASN THR HIS GLU TRP GLN TYR TYR ILE SER GLY SEQRES 23 A 390 LYS ALA ARG MET THR VAL PHE ALA SER ASP GLY HIS ALA SEQRES 24 A 390 ARG THR PHE ASN TYR GLN ALA GLY ASP VAL GLY TYR VAL SEQRES 25 A 390 PRO PHE ALA MET GLY HIS TYR VAL GLU ASN ILE GLY ASP SEQRES 26 A 390 GLU PRO LEU VAL PHE LEU GLU ILE PHE LYS ASP ASP HIS SEQRES 27 A 390 TYR ALA ASP VAL SER LEU ASN GLN TRP LEU ALA MET LEU SEQRES 28 A 390 PRO GLU THR PHE VAL GLN ALA HIS LEU ASP LEU GLY LYS SEQRES 29 A 390 ASP PHE THR ASP VAL LEU SER LYS GLU LYS HIS PRO VAL SEQRES 30 A 390 VAL LYS LYS LYS CYS SER LYS HIS HIS HIS HIS HIS HIS HET CO A 401 1 HET CO A 402 1 HET OXL A 403 6 HET NA A 404 1 HETNAM CO COBALT (II) ION HETNAM OXL OXALATE ION HETNAM NA SODIUM ION FORMUL 2 CO 2(CO 2+) FORMUL 4 OXL C2 O4 2- FORMUL 5 NA NA 1+ FORMUL 6 HOH *104(H2 O) HELIX 1 AA1 ASN A 24 ASN A 31 1 8 HELIX 2 AA2 ASN A 31 VAL A 36 1 6 HELIX 3 AA3 SER A 53 THR A 55 5 3 HELIX 4 AA4 LEU A 167 HIS A 173 1 7 HELIX 5 AA5 PRO A 175 GLY A 184 1 10 HELIX 6 AA6 LYS A 187 SER A 191 5 5 HELIX 7 AA7 SER A 208 ASP A 212 5 5 HELIX 8 AA8 LEU A 230 GLN A 232 5 3 HELIX 9 AA9 LEU A 344 MET A 350 1 7 HELIX 10 AB1 PRO A 352 ASP A 361 1 10 HELIX 11 AB2 GLY A 363 ASP A 368 1 6 SHEET 1 AA1 2 ILE A 11 ARG A 12 0 SHEET 2 AA1 2 LYS A 15 GLY A 16 -1 O LYS A 15 N ARG A 12 SHEET 1 AA2 7 LYS A 49 SER A 51 0 SHEET 2 AA2 7 ASP A 308 VAL A 312 -1 O VAL A 309 N PHE A 50 SHEET 3 AA2 7 GLU A 279 SER A 285 -1 N GLU A 279 O VAL A 312 SHEET 4 AA2 7 LEU A 328 PHE A 334 -1 O ILE A 333 N TRP A 280 SHEET 5 AA2 7 ALA A 257 VAL A 263 -1 N VAL A 263 O LEU A 328 SHEET 6 AA2 7 GLY A 240 ALA A 245 -1 N LYS A 241 O THR A 262 SHEET 7 AA2 7 ILE A 235 SER A 237 -1 N ILE A 235 O VAL A 242 SHEET 1 AA3 6 ARG A 58 GLU A 60 0 SHEET 2 AA3 6 GLY A 63 VAL A 68 -1 O GLY A 63 N GLU A 60 SHEET 3 AA3 6 ALA A 80 LEU A 86 -1 O ASN A 83 N ARG A 66 SHEET 4 AA3 6 HIS A 140 PHE A 155 -1 O LEU A 153 N VAL A 82 SHEET 5 AA3 6 ILE A 91 TRP A 96 -1 N ARG A 92 O ILE A 142 SHEET 6 AA3 6 ILE A 200 PHE A 201 -1 O PHE A 201 N ILE A 91 SHEET 1 AA4 5 PHE A 165 GLN A 166 0 SHEET 2 AA4 5 ILE A 91 TRP A 96 -1 N TRP A 96 O PHE A 165 SHEET 3 AA4 5 HIS A 140 PHE A 155 -1 O ILE A 142 N ARG A 92 SHEET 4 AA4 5 GLU A 101 VAL A 115 -1 N ARG A 111 O GLN A 143 SHEET 5 AA4 5 SER A 121 VAL A 126 -1 O PHE A 122 N ILE A 114 SHEET 1 AA5 4 SER A 121 VAL A 126 0 SHEET 2 AA5 4 GLU A 101 VAL A 115 -1 N ILE A 114 O PHE A 122 SHEET 3 AA5 4 ASP A 130 PHE A 134 -1 O PHE A 134 N GLU A 101 SHEET 4 AA5 4 THR A 226 ARG A 228 -1 O TYR A 227 N LEU A 131 SHEET 1 AA6 5 ALA A 299 GLN A 305 0 SHEET 2 AA6 5 LYS A 287 PHE A 293 -1 N VAL A 292 O ARG A 300 SHEET 3 AA6 5 GLY A 317 ASN A 322 -1 O GLY A 317 N PHE A 293 SHEET 4 AA6 5 ALA A 267 TRP A 273 -1 N ARG A 269 O VAL A 320 SHEET 5 AA6 5 VAL A 342 SER A 343 -1 O VAL A 342 N TRP A 273 SHEET 1 AA7 5 ALA A 299 GLN A 305 0 SHEET 2 AA7 5 LYS A 287 PHE A 293 -1 N VAL A 292 O ARG A 300 SHEET 3 AA7 5 GLY A 317 ASN A 322 -1 O GLY A 317 N PHE A 293 SHEET 4 AA7 5 ALA A 267 TRP A 273 -1 N ARG A 269 O VAL A 320 SHEET 5 AA7 5 VAL A 377 LYS A 379 -1 O VAL A 378 N MET A 268 LINK NE2 HIS A 95 CO CO A 401 1555 1555 2.25 LINK NE2 HIS A 97 CO CO A 401 1555 1555 2.16 LINK OE1 GLU A 101 CO CO A 401 1555 1555 2.05 LINK NE2 HIS A 140 CO CO A 401 1555 1555 2.08 LINK NE2 HIS A 272 CO CO A 402 1555 1555 2.40 LINK NE2 HIS A 274 CO CO A 402 1555 1555 2.12 LINK OE1 GLU A 279 CO CO A 402 1555 1555 1.90 LINK NE2 HIS A 318 CO CO A 402 1555 1555 1.92 LINK CO CO A 401 O HOH A 516 1555 1555 2.43 LINK CO CO A 402 O HOH A 524 1555 1555 1.88 LINK NA NA A 404 O HOH A 543 1555 1555 3.02 SITE 1 AC1 6 HIS A 95 HIS A 97 GLU A 101 HIS A 140 SITE 2 AC1 6 OXL A 403 HOH A 516 SITE 1 AC2 7 HIS A 272 HIS A 274 GLU A 279 HIS A 318 SITE 2 AC2 7 GLU A 332 HOH A 503 HOH A 524 SITE 1 AC3 11 MET A 84 ARG A 92 HIS A 95 HIS A 97 SITE 2 AC3 11 GLU A 101 HIS A 140 LEU A 153 THR A 164 SITE 3 AC3 11 CO A 401 HOH A 513 HOH A 516 SITE 1 AC4 1 HOH A 543 CRYST1 154.619 154.619 121.954 90.00 90.00 120.00 H 3 2 18 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 0.006468 0.003734 0.000000 0.00000 SCALE2 0.000000 0.007468 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008200 0.00000