HEADER OXIDOREDUCTASE 02-JUN-19 5BKB TITLE CRYSTAL STRUCTURE OF AAD-1 IN COMPLEX WITH (R)-DICHLORPROP, MN(II), TITLE 2 AND 2-OXOGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: (R)-PHENOXYPROPIONATE/ALPHA-KETOGLUTARATE-DIOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RDPA,(R)-DICHLORPROP/(R)-MECOPROP DIOXYGENASE,ALPHA- COMPND 5 KETOGLUTARATE-DEPENDENT DIOXYGENASE,DICHLORPROP/ALPHA-KETOGLUTARATE- COMPND 6 DIOXYGENASE,MECOPROP/ALPHA-KETOGLUTARATE-DIOXYGENASE; COMPND 7 EC: 1.14.11.44; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DELFTIA ACIDOVORANS; SOURCE 3 ORGANISM_COMMON: PSEUDOMONAS ACIDOVORANS; SOURCE 4 ORGANISM_TAXID: 80866; SOURCE 5 GENE: RDPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIOXYGENASE, HERBICIDE DEGRADATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.CHEKAN,S.K.NAIR REVDAT 4 27-SEP-23 5BKB 1 REMARK LINK REVDAT 3 17-JUL-19 5BKB 1 JRNL REVDAT 2 03-JUL-19 5BKB 1 JRNL REVDAT 1 12-JUN-19 5BKB 0 JRNL AUTH J.R.CHEKAN,C.ONGPIPATTANAKUL,T.R.WRIGHT,B.ZHANG, JRNL AUTH 2 J.M.BOLLINGER JR.,L.J.RAJAKOVICH,C.KREBS,R.M.CICCHILLO, JRNL AUTH 3 S.K.NAIR JRNL TITL MOLECULAR BASIS FOR ENANTIOSELECTIVE HERBICIDE DEGRADATION JRNL TITL 2 IMPARTED BY ARYLOXYALKANOATE DIOXYGENASES IN TRANSGENIC JRNL TITL 3 PLANTS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 13299 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31209034 JRNL DOI 10.1073/PNAS.1900711116 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 80828 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 3956 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 54.2279 - 4.8031 0.99 2963 132 0.1615 0.1813 REMARK 3 2 4.8031 - 3.8127 1.00 2837 145 0.1263 0.1495 REMARK 3 3 3.8127 - 3.3308 1.00 2788 158 0.1481 0.1865 REMARK 3 4 3.3308 - 3.0263 1.00 2767 160 0.1525 0.1770 REMARK 3 5 3.0263 - 2.8094 1.00 2771 143 0.1687 0.2076 REMARK 3 6 2.8094 - 2.6438 1.00 2777 133 0.1654 0.2146 REMARK 3 7 2.6438 - 2.5114 1.00 2757 131 0.1629 0.1811 REMARK 3 8 2.5114 - 2.4021 1.00 2783 124 0.1622 0.2106 REMARK 3 9 2.4021 - 2.3096 1.00 2738 141 0.1586 0.2157 REMARK 3 10 2.3096 - 2.2299 1.00 2762 139 0.1563 0.2190 REMARK 3 11 2.2299 - 2.1602 1.00 2723 151 0.1603 0.2035 REMARK 3 12 2.1602 - 2.0984 1.00 2738 138 0.1567 0.1930 REMARK 3 13 2.0984 - 2.0432 1.00 2725 141 0.1570 0.2034 REMARK 3 14 2.0432 - 1.9933 1.00 2710 155 0.1625 0.1764 REMARK 3 15 1.9933 - 1.9480 1.00 2716 153 0.1585 0.1933 REMARK 3 16 1.9480 - 1.9065 1.00 2729 143 0.1690 0.1967 REMARK 3 17 1.9065 - 1.8684 1.00 2725 146 0.1682 0.2049 REMARK 3 18 1.8684 - 1.8331 1.00 2706 159 0.1765 0.2339 REMARK 3 19 1.8331 - 1.8004 1.00 2716 128 0.1755 0.2226 REMARK 3 20 1.8004 - 1.7699 1.00 2743 141 0.1734 0.2400 REMARK 3 21 1.7699 - 1.7413 1.00 2678 151 0.1794 0.2288 REMARK 3 22 1.7413 - 1.7145 1.00 2711 149 0.1893 0.2412 REMARK 3 23 1.7145 - 1.6893 1.00 2706 144 0.1994 0.2404 REMARK 3 24 1.6893 - 1.6655 1.00 2735 140 0.1996 0.2364 REMARK 3 25 1.6655 - 1.6430 1.00 2721 126 0.1994 0.2326 REMARK 3 26 1.6430 - 1.6217 1.00 2714 130 0.2111 0.2204 REMARK 3 27 1.6217 - 1.6014 1.00 2738 120 0.2111 0.2572 REMARK 3 28 1.6014 - 1.5821 1.00 2695 135 0.2411 0.2534 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.910 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 : 0.011 4676 REMARK 3 ANGLE : 1.249 6389 REMARK 3 CHIRALITY : 0.063 701 REMARK 3 PLANARITY : 0.007 839 REMARK 3 DIHEDRAL : 13.790 1740 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 5BKB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1001310067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80901 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 85.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.95600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 1GQW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350 0.3M LISO4 0.1M BICINE PH REMARK 280 9.0 8 MG/ML AAD-1 CRYO: 15% GLYCEROL, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 42.92500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.90200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.92500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.90200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 2910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 85.85000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 97.80400 REMARK 350 BIOMT3 2 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 HIS A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 LEU A 5 REMARK 465 SER A 6 REMARK 465 MET B 1 REMARK 465 HIS B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 4 REMARK 465 LEU B 5 REMARK 465 SER B 6 REMARK 465 PRO B 7 REMARK 465 LEU B 8 REMARK 465 SER B 9 REMARK 465 GLN B 10 REMARK 465 TYR B 175 REMARK 465 GLN B 176 REMARK 465 ALA B 177 REMARK 465 GLN B 178 REMARK 465 ASN B 179 REMARK 465 ARG B 180 REMARK 465 ARG B 181 REMARK 465 PHE B 182 REMARK 465 SER B 183 REMARK 465 ASN B 184 REMARK 465 THR B 185 REMARK 465 SER B 186 REMARK 465 VAL B 187 REMARK 465 LYS B 188 REMARK 465 VAL B 189 REMARK 465 MET B 190 REMARK 465 ASP B 191 REMARK 465 VAL B 192 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 OE1 GLN A 219 O HOH A 601 1.97 REMARK 500 O HOH A 968 O HOH A 1017 2.04 REMARK 500 O HOH B 620 O HOH B 738 2.05 REMARK 500 O HOH B 760 O HOH B 761 2.07 REMARK 500 O ARG B 104 O HOH B 601 2.07 REMARK 500 O HOH A 900 O HOH A 905 2.09 REMARK 500 O HOH A 813 O HOH A 963 2.09 REMARK 500 O HOH B 727 O HOH B 838 2.10 REMARK 500 OE1 GLU B 87 O HOH B 602 2.10 REMARK 500 O4 PEG B 504 O HOH B 603 2.11 REMARK 500 O HOH A 730 O HOH A 776 2.13 REMARK 500 O HOH B 862 O HOH B 873 2.14 REMARK 500 O HOH B 765 O HOH B 897 2.17 REMARK 500 O HOH A 713 O HOH A 861 2.18 REMARK 500 O HOH B 889 O HOH B 899 2.18 REMARK 500 O HOH A 910 O HOH A 935 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 911 O HOH B 811 2665 2.19 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 GLN A 53 -32.02 73.50 REMARK 500 ASP A 78 83.80 -154.31 REMARK 500 PHE A 171 20.04 -154.12 REMARK 500 TYR A 276 37.82 -141.46 REMARK 500 PHE B 12 90.41 59.86 REMARK 500 GLN B 53 -34.08 76.62 REMARK 500 ASP B 108 30.90 -84.45 REMARK 500 PHE B 171 25.35 -142.34 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 A1023 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A1024 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1025 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A1026 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A1027 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A1028 DISTANCE = 6.65 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 111 NE2 REMARK 620 2 ASP A 113 OD1 96.5 REMARK 620 3 HIS A 270 NE2 90.4 96.8 REMARK 620 4 AKG A 502 O1 150.2 100.9 111.2 REMARK 620 5 AKG A 502 O5 88.7 172.1 89.1 71.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 111 NE2 REMARK 620 2 ASP B 113 OD1 95.1 REMARK 620 3 HIS B 270 NE2 85.6 94.6 REMARK 620 4 AKG B 502 O2 158.1 104.1 103.0 REMARK 620 5 AKG B 502 O5 89.1 175.7 87.0 71.6 REMARK 620 6 HOH B 815 O 85.6 92.5 169.1 83.1 86.5 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 MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FTV 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 MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5BKD RELATED DB: PDB REMARK 900 RELATED ID: 5BKC RELATED DB: PDB REMARK 900 RELATED ID: 5BK9 RELATED DB: PDB REMARK 900 RELATED ID: 5BKE RELATED DB: PDB DBREF 5BKB A 1 295 UNP P83310 RDPA_DELAC 1 295 DBREF 5BKB B 1 295 UNP P83310 RDPA_DELAC 1 295 SEQRES 1 A 295 MET HIS ALA ALA LEU SER PRO LEU SER GLN ARG PHE GLU SEQRES 2 A 295 ARG ILE ALA VAL GLN PRO LEU THR GLY VAL LEU GLY ALA SEQRES 3 A 295 GLU ILE THR GLY VAL ASP LEU ARG GLU PRO LEU ASP ASP SEQRES 4 A 295 SER THR TRP ASN GLU ILE LEU ASP ALA PHE HIS THR TYR SEQRES 5 A 295 GLN VAL ILE TYR PHE PRO GLY GLN ALA ILE THR ASN GLU SEQRES 6 A 295 GLN HIS ILE ALA PHE SER ARG ARG PHE GLY PRO VAL ASP SEQRES 7 A 295 PRO VAL PRO LEU LEU LYS SER ILE GLU GLY TYR PRO GLU SEQRES 8 A 295 VAL GLN MET ILE ARG ARG GLU ALA ASN GLU SER GLY ARG SEQRES 9 A 295 VAL ILE GLY ASP ASP TRP HIS THR ASP SER THR PHE LEU SEQRES 10 A 295 ASP ALA PRO PRO ALA ALA VAL VAL MET ARG ALA ILE ASP SEQRES 11 A 295 VAL PRO GLU HIS GLY GLY ASP THR GLY PHE LEU SER MET SEQRES 12 A 295 TYR THR ALA TRP GLU THR LEU SER PRO THR MET GLN ALA SEQRES 13 A 295 THR ILE GLU GLY LEU ASN VAL VAL HIS SER ALA THR ARG SEQRES 14 A 295 VAL PHE GLY SER LEU TYR GLN ALA GLN ASN ARG ARG PHE SEQRES 15 A 295 SER ASN THR SER VAL LYS VAL MET ASP VAL ASP ALA GLY SEQRES 16 A 295 ASP ARG GLU THR VAL HIS PRO LEU VAL VAL THR HIS PRO SEQRES 17 A 295 GLY SER GLY ARG LYS GLY LEU TYR VAL ASN GLN VAL TYR SEQRES 18 A 295 CYS GLN ARG ILE GLU GLY MET THR ASP ALA GLU SER LYS SEQRES 19 A 295 PRO LEU LEU GLN PHE LEU TYR GLU HIS ALA THR ARG PHE SEQRES 20 A 295 ASP PHE THR CYS ARG VAL ARG TRP LYS LYS ASP GLN VAL SEQRES 21 A 295 LEU VAL TRP ASP ASN LEU CYS THR MET HIS ARG ALA VAL SEQRES 22 A 295 PRO ASP TYR ALA GLY LYS PHE ARG TYR LEU THR ARG THR SEQRES 23 A 295 THR VAL GLY GLY VAL ARG PRO ALA ARG SEQRES 1 B 295 MET HIS ALA ALA LEU SER PRO LEU SER GLN ARG PHE GLU SEQRES 2 B 295 ARG ILE ALA VAL GLN PRO LEU THR GLY VAL LEU GLY ALA SEQRES 3 B 295 GLU ILE THR GLY VAL ASP LEU ARG GLU PRO LEU ASP ASP SEQRES 4 B 295 SER THR TRP ASN GLU ILE LEU ASP ALA PHE HIS THR TYR SEQRES 5 B 295 GLN VAL ILE TYR PHE PRO GLY GLN ALA ILE THR ASN GLU SEQRES 6 B 295 GLN HIS ILE ALA PHE SER ARG ARG PHE GLY PRO VAL ASP SEQRES 7 B 295 PRO VAL PRO LEU LEU LYS SER ILE GLU GLY TYR PRO GLU SEQRES 8 B 295 VAL GLN MET ILE ARG ARG GLU ALA ASN GLU SER GLY ARG SEQRES 9 B 295 VAL ILE GLY ASP ASP TRP HIS THR ASP SER THR PHE LEU SEQRES 10 B 295 ASP ALA PRO PRO ALA ALA VAL VAL MET ARG ALA ILE ASP SEQRES 11 B 295 VAL PRO GLU HIS GLY GLY ASP THR GLY PHE LEU SER MET SEQRES 12 B 295 TYR THR ALA TRP GLU THR LEU SER PRO THR MET GLN ALA SEQRES 13 B 295 THR ILE GLU GLY LEU ASN VAL VAL HIS SER ALA THR ARG SEQRES 14 B 295 VAL PHE GLY SER LEU TYR GLN ALA GLN ASN ARG ARG PHE SEQRES 15 B 295 SER ASN THR SER VAL LYS VAL MET ASP VAL ASP ALA GLY SEQRES 16 B 295 ASP ARG GLU THR VAL HIS PRO LEU VAL VAL THR HIS PRO SEQRES 17 B 295 GLY SER GLY ARG LYS GLY LEU TYR VAL ASN GLN VAL TYR SEQRES 18 B 295 CYS GLN ARG ILE GLU GLY MET THR ASP ALA GLU SER LYS SEQRES 19 B 295 PRO LEU LEU GLN PHE LEU TYR GLU HIS ALA THR ARG PHE SEQRES 20 B 295 ASP PHE THR CYS ARG VAL ARG TRP LYS LYS ASP GLN VAL SEQRES 21 B 295 LEU VAL TRP ASP ASN LEU CYS THR MET HIS ARG ALA VAL SEQRES 22 B 295 PRO ASP TYR ALA GLY LYS PHE ARG TYR LEU THR ARG THR SEQRES 23 B 295 THR VAL GLY GLY VAL ARG PRO ALA ARG HET MN A 501 1 HET AKG A 502 10 HET FTV A 503 14 HET SO4 A 504 5 HET SO4 A 505 5 HET MN B 501 1 HET AKG B 502 10 HET SO4 B 503 5 HET PEG B 504 7 HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM FTV (2R)-2-(2,4-DICHLOROPHENOXY)PROPANOIC ACID HETNAM SO4 SULFATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 MN 2(MN 2+) FORMUL 4 AKG 2(C5 H6 O5) FORMUL 5 FTV C9 H8 CL2 O3 FORMUL 6 SO4 3(O4 S 2-) FORMUL 11 PEG C4 H10 O3 FORMUL 12 HOH *734(H2 O) HELIX 1 AA1 PRO A 7 PHE A 12 1 6 HELIX 2 AA2 ASP A 38 GLN A 53 1 16 HELIX 3 AA3 THR A 63 ARG A 73 1 11 HELIX 4 AA4 MET A 143 THR A 149 1 7 HELIX 5 AA5 SER A 151 GLU A 159 1 9 HELIX 6 AA6 ALA A 167 GLY A 172 1 6 HELIX 7 AA7 GLY A 172 ALA A 177 1 6 HELIX 8 AA8 ASP A 191 ARG A 197 1 7 HELIX 9 AA9 THR A 229 THR A 245 1 17 HELIX 10 AB1 ARG A 246 ASP A 248 5 3 HELIX 11 AB2 ASP B 38 GLN B 53 1 16 HELIX 12 AB3 THR B 63 ARG B 73 1 11 HELIX 13 AB4 MET B 143 THR B 149 1 7 HELIX 14 AB5 SER B 151 GLU B 159 1 9 HELIX 15 AB6 THR B 229 THR B 245 1 17 HELIX 16 AB7 ARG B 246 ASP B 248 5 3 SHEET 1 AA1 8 ALA A 16 PRO A 19 0 SHEET 2 AA1 8 ALA A 26 THR A 29 -1 O GLU A 27 N GLN A 18 SHEET 3 AA1 8 VAL A 54 PHE A 57 1 O TYR A 56 N ILE A 28 SHEET 4 AA1 8 VAL A 260 ASP A 264 -1 O VAL A 260 N PHE A 57 SHEET 5 AA1 8 ALA A 123 ASP A 130 -1 N MET A 126 O LEU A 261 SHEET 6 AA1 8 ARG A 281 VAL A 288 -1 O THR A 284 N ARG A 127 SHEET 7 AA1 8 TYR A 89 ARG A 97 -1 N ILE A 95 O LEU A 283 SHEET 8 AA1 8 SER A 85 ILE A 86 -1 N ILE A 86 O VAL A 92 SHEET 1 AA2 3 THR A 250 VAL A 253 0 SHEET 2 AA2 3 THR A 138 SER A 142 -1 N THR A 138 O VAL A 253 SHEET 3 AA2 3 THR A 268 ALA A 272 -1 O ARG A 271 N GLY A 139 SHEET 1 AA3 3 THR A 199 PRO A 202 0 SHEET 2 AA3 3 ASN A 162 HIS A 165 -1 N HIS A 165 O THR A 199 SHEET 3 AA3 3 CYS A 222 ILE A 225 -1 O GLN A 223 N VAL A 164 SHEET 1 AA4 2 VAL A 204 THR A 206 0 SHEET 2 AA4 2 LYS A 213 LEU A 215 -1 O GLY A 214 N VAL A 205 SHEET 1 AA5 8 ALA B 16 PRO B 19 0 SHEET 2 AA5 8 ALA B 26 THR B 29 -1 O GLU B 27 N GLN B 18 SHEET 3 AA5 8 VAL B 54 PHE B 57 1 O TYR B 56 N ILE B 28 SHEET 4 AA5 8 VAL B 260 ASP B 264 -1 O VAL B 260 N PHE B 57 SHEET 5 AA5 8 ALA B 123 ASP B 130 -1 N MET B 126 O LEU B 261 SHEET 6 AA5 8 ARG B 281 VAL B 288 -1 O TYR B 282 N ASP B 130 SHEET 7 AA5 8 TYR B 89 ARG B 97 -1 N ILE B 95 O LEU B 283 SHEET 8 AA5 8 SER B 85 ILE B 86 -1 N ILE B 86 O VAL B 92 SHEET 1 AA6 3 THR B 250 VAL B 253 0 SHEET 2 AA6 3 THR B 138 SER B 142 -1 N THR B 138 O VAL B 253 SHEET 3 AA6 3 THR B 268 ALA B 272 -1 O ARG B 271 N GLY B 139 SHEET 1 AA7 3 THR B 199 PRO B 202 0 SHEET 2 AA7 3 ASN B 162 HIS B 165 -1 N HIS B 165 O THR B 199 SHEET 3 AA7 3 CYS B 222 ILE B 225 -1 O GLN B 223 N VAL B 164 SHEET 1 AA8 2 VAL B 204 THR B 206 0 SHEET 2 AA8 2 LYS B 213 LEU B 215 -1 O GLY B 214 N VAL B 205 LINK NE2 HIS A 111 MN MN A 501 1555 1555 2.22 LINK OD1 ASP A 113 MN MN A 501 1555 1555 2.08 LINK NE2 HIS A 270 MN MN A 501 1555 1555 2.23 LINK MN MN A 501 O1 AKG A 502 1555 1555 2.02 LINK MN MN A 501 O5 AKG A 502 1555 1555 2.43 LINK NE2 HIS B 111 MN MN B 501 1555 1555 2.23 LINK OD1 ASP B 113 MN MN B 501 1555 1555 2.15 LINK NE2 HIS B 270 MN MN B 501 1555 1555 2.26 LINK MN MN B 501 O2 AKG B 502 1555 1555 2.03 LINK MN MN B 501 O5 AKG B 502 1555 1555 2.44 LINK MN MN B 501 O HOH B 815 1555 1555 2.48 SITE 1 AC1 4 HIS A 111 ASP A 113 HIS A 270 AKG A 502 SITE 1 AC2 13 ILE A 95 ILE A 106 GLY A 107 HIS A 111 SITE 2 AC2 13 ASP A 113 MET A 126 THR A 138 HIS A 270 SITE 3 AC2 13 ARG A 281 ARG A 285 MN A 501 HOH A 668 SITE 4 AC2 13 HOH A 712 SITE 1 AC3 7 LEU A 82 ARG A 104 GLY A 107 HIS A 111 SITE 2 AC3 7 ASP A 113 SER A 114 TYR A 221 SITE 1 AC4 8 ARG A 34 GLN A 66 ARG A 224 GLY A 227 SITE 2 AC4 8 HOH A 614 HOH A 648 HOH A 667 HOH A 867 SITE 1 AC5 9 TRP A 110 ARG A 271 HOH A 604 HOH A 613 SITE 2 AC5 9 HOH A 724 ARG B 246 PHE B 247 HOH B 635 SITE 3 AC5 9 HOH B 743 SITE 1 AC6 5 HIS B 111 ASP B 113 HIS B 270 AKG B 502 SITE 2 AC6 5 HOH B 815 SITE 1 AC7 13 ILE B 95 GLY B 107 HIS B 111 ASP B 113 SITE 2 AC7 13 MET B 126 THR B 138 HIS B 270 ARG B 281 SITE 3 AC7 13 ARG B 285 MN B 501 HOH B 657 HOH B 790 SITE 4 AC7 13 HOH B 815 SITE 1 AC8 6 ARG B 224 GLU B 226 GLY B 227 LYS B 257 SITE 2 AC8 6 HOH B 625 HOH B 690 SITE 1 AC9 9 PHE A 247 ASP B 109 TRP B 110 GLN B 219 SITE 2 AC9 9 ARG B 271 HOH B 603 HOH B 613 HOH B 695 SITE 3 AC9 9 HOH B 778 CRYST1 85.850 97.804 69.881 90.00 90.00 90.00 P 21 21 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 0.011648 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010225 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014310 0.00000