HEADER LYASE 03-JUL-03 1O4T TITLE CRYSTAL STRUCTURE OF A PREDICTED OXALATE DECARBOXYLASE (TM1287) FROM TITLE 2 THERMOTOGA MARITIMA AT 1.95 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE OXALATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: TM1287; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS DOUBLE-STRANDED BETA-HELIX FOLD, STRUCTURAL GENOMICS, JOINT CENTER KEYWDS 2 FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, KEYWDS 3 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 12 20-SEP-23 1O4T 1 REMARK REVDAT 11 25-JAN-23 1O4T 1 REMARK SEQADV LINK REVDAT 10 18-JUL-18 1O4T 1 REMARK REVDAT 9 04-OCT-17 1O4T 1 REMARK REVDAT 8 13-JUL-11 1O4T 1 VERSN REVDAT 7 23-MAR-11 1O4T 1 HEADER TITLE KEYWDS REVDAT 6 24-FEB-09 1O4T 1 VERSN REVDAT 5 20-SEP-05 1O4T 1 JRNL REVDAT 4 18-JAN-05 1O4T 1 AUTHOR KEYWDS REMARK REVDAT 3 03-AUG-04 1O4T 1 JRNL REVDAT 2 22-JUL-03 1O4T 1 REMARK REVDAT 1 15-JUL-03 1O4T 0 JRNL AUTH R.SCHWARZENBACHER,F.VON DELFT,L.JAROSZEWSKI,P.ABDUBEK, JRNL AUTH 2 E.AMBING,T.BIORAC,L.S.BRINEN,J.M.CANAVES,J.CAMBELL,H.J.CHIU, JRNL AUTH 3 X.DAI,A.M.DEACON,M.DIDONATO,M.A.ELSLIGER,S.ESHAGI,R.FLOYD, JRNL AUTH 4 A.GODZIK,C.GRITTINI,S.K.GRZECHNIK,E.HAMPTON,C.KARLAK, JRNL AUTH 5 H.E.KLOCK,E.KOESEMA,J.S.KOVARIK,A.KREUSCH,P.KUHN,S.A.LESLEY, JRNL AUTH 6 I.LEVIN,D.MCMULLAN,T.M.MCPHILLIPS,M.D.MILLER,A.MORSE,K.MOY, JRNL AUTH 7 J.OUYANG,R.PAGE,K.QUIJANO,A.ROBB,G.SPRAGGON,R.C.STEVENS, JRNL AUTH 8 H.VAN DEN BEDEM,J.VELASQUEZ,J.VINCENT,X.WANG,B.WEST,G.WOLF, JRNL AUTH 9 Q.XU,K.O.HODGSON,J.WOOLEY,I.A.WILSON JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE OXALATE DECARBOXYLASE JRNL TITL 2 (TM1287) FROM THERMOTOGA MARITIMA AT 1.95 A RESOLUTION JRNL REF PROTEINS V. 56 392 2004 JRNL REFN ISSN 0887-3585 JRNL PMID 15211523 JRNL DOI 10.1002/PROT.20016 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 16875 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 883 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1078 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1772 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 198 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 36.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.90000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.66000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.153 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.542 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1823 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1667 ; 0.010 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2450 ; 1.568 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3887 ; 0.849 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 228 ; 6.172 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;33.595 ;24.074 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 330 ;14.126 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;11.733 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 270 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2033 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 354 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 304 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1650 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1193 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 134 ; 0.207 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 7 ; 0.147 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 27 ; 0.239 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.269 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1136 ; 0.802 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1823 ; 1.483 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 687 ; 2.675 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 627 ; 4.474 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 121 REMARK 3 RESIDUE RANGE : B 7 B 121 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3219 -0.1822 16.2354 REMARK 3 T TENSOR REMARK 3 T11: -0.1642 T22: -0.1800 REMARK 3 T33: -0.1254 T12: -0.0243 REMARK 3 T13: -0.0371 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 2.4919 L22: 1.2500 REMARK 3 L33: 4.4463 L12: 1.1049 REMARK 3 L13: -1.9792 L23: -1.8341 REMARK 3 S TENSOR REMARK 3 S11: -0.1108 S12: 0.2669 S13: -0.0363 REMARK 3 S21: -0.1352 S22: 0.1837 S23: 0.0443 REMARK 3 S31: -0.0197 S32: -0.2088 S33: -0.0729 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. METAL IDENTIFIED BY A) HOMOLOGY TO REMARK 3 1J58 B) BEST AGREEMENT OF REFINED B-FACTOR WITH LIGATING REMARK 3 RESIDUES. 2. OXALATE IDENIFIED BASED ON HOMOLOGY TO 1J58. HIGH REMARK 3 BFACTORS INDICATE PARTIAL OCCUPANCY, WHICH WAS NOT MODELED. C- C REMARK 3 BOND PLANARITY WAS NOT RESTRAINED DURING REFINEMENT. 3. ARG23 REMARK 3 HAS CLOSELY-BOUND WATER; DENSITY SUGGESTS POSSIBLE OMEGA - REMARK 3 HYDROXYLATED ARGININE. 4. UNEXPLAINED CONTINUOUS DENSITY MODELED REMARK 3 AS WATER CHAINS. 5. HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 1O4T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000001804. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.983967 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(311) BENT REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : FLAT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 4.2), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17758 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 25.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.55500 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1FI2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % PEG 6000, 1.0 M LICL, 0.1 M MES, REMARK 280 PH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, TEMPERATURE 293K, REMARK 280 PH 6.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 44.56600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.86900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.56600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.86900 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: 3730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 3 REMARK 465 GLY A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 MET B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 ASP B -8 REMARK 465 LYS B -7 REMARK 465 ILE B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 GLU B 3 REMARK 465 GLY B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 84 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 429 O HOH B 467 1.83 REMARK 500 O HOH A 439 O HOH B 426 1.97 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 B 494 O HOH B 507 4546 2.12 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 ALA A 90 129.15 -38.90 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 MN A 300 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 HIS A 63 NE2 94.4 REMARK 620 3 GLU A 68 OE2 171.5 79.7 REMARK 620 4 HIS A 102 NE2 91.3 97.1 95.5 REMARK 620 5 OXL A 400 O4 86.0 90.5 87.9 172.2 REMARK 620 6 OXL A 400 O3 92.9 166.7 91.8 93.8 79.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 61 NE2 REMARK 620 2 HIS B 63 NE2 99.5 REMARK 620 3 GLU B 68 OE2 178.6 80.4 REMARK 620 4 HIS B 102 NE2 88.4 96.0 93.1 REMARK 620 5 OXL B 401 O3 91.4 86.4 87.2 177.6 REMARK 620 6 OXL B 401 O4 92.0 163.0 87.8 96.8 80.9 REMARK 620 N 1 2 3 4 5 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXL A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXL B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 283151 RELATED DB: TARGETDB DBREF 1O4T A 1 121 UNP Q9X113 Q9X113_THEMA 1 121 DBREF 1O4T B 1 121 UNP Q9X113 Q9X113_THEMA 1 121 SEQADV 1O4T MET A -11 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T GLY A -10 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T SER A -9 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T ASP A -8 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T LYS A -7 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T ILE A -6 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS A -5 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS A -4 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS A -3 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS A -2 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS A -1 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS A 0 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T MET B -11 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T GLY B -10 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T SER B -9 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T ASP B -8 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T LYS B -7 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T ILE B -6 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS B -5 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS B -4 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS B -3 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS B -2 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS B -1 UNP Q9X113 EXPRESSION TAG SEQADV 1O4T HIS B 0 UNP Q9X113 EXPRESSION TAG SEQRES 1 A 133 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 A 133 LYS GLU GLY THR GLY MET VAL VAL ARG SER SER GLU ILE SEQRES 3 A 133 THR PRO GLU ARG ILE SER ASN MET ARG GLY GLY LYS GLY SEQRES 4 A 133 GLU VAL GLU MET ALA HIS LEU LEU SER LYS GLU ALA MET SEQRES 5 A 133 HIS ASN LYS ALA ARG LEU PHE ALA ARG MET LYS LEU PRO SEQRES 6 A 133 PRO GLY SER SER VAL GLY LEU HIS LYS HIS GLU GLY GLU SEQRES 7 A 133 PHE GLU ILE TYR TYR ILE LEU LEU GLY GLU GLY VAL PHE SEQRES 8 A 133 HIS ASP ASN GLY LYS ASP VAL PRO ILE LYS ALA GLY ASP SEQRES 9 A 133 VAL CYS PHE THR ASP SER GLY GLU SER HIS SER ILE GLU SEQRES 10 A 133 ASN THR GLY ASN THR ASP LEU GLU PHE LEU ALA VAL ILE SEQRES 11 A 133 ILE LEU LEU SEQRES 1 B 133 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 B 133 LYS GLU GLY THR GLY MET VAL VAL ARG SER SER GLU ILE SEQRES 3 B 133 THR PRO GLU ARG ILE SER ASN MET ARG GLY GLY LYS GLY SEQRES 4 B 133 GLU VAL GLU MET ALA HIS LEU LEU SER LYS GLU ALA MET SEQRES 5 B 133 HIS ASN LYS ALA ARG LEU PHE ALA ARG MET LYS LEU PRO SEQRES 6 B 133 PRO GLY SER SER VAL GLY LEU HIS LYS HIS GLU GLY GLU SEQRES 7 B 133 PHE GLU ILE TYR TYR ILE LEU LEU GLY GLU GLY VAL PHE SEQRES 8 B 133 HIS ASP ASN GLY LYS ASP VAL PRO ILE LYS ALA GLY ASP SEQRES 9 B 133 VAL CYS PHE THR ASP SER GLY GLU SER HIS SER ILE GLU SEQRES 10 B 133 ASN THR GLY ASN THR ASP LEU GLU PHE LEU ALA VAL ILE SEQRES 11 B 133 ILE LEU LEU HET MN A 300 1 HET OXL A 400 6 HET MN B 301 1 HET OXL B 401 6 HETNAM MN MANGANESE (II) ION HETNAM OXL OXALATE ION FORMUL 3 MN 2(MN 2+) FORMUL 4 OXL 2(C2 O4 2-) FORMUL 7 HOH *198(H2 O) HELIX 1 1 SER A 12 ILE A 14 5 3 HELIX 2 2 SER B 12 ILE B 14 5 3 SHEET 1 A 7 VAL A 8 ARG A 10 0 SHEET 2 A 7 ASP B 92 THR B 96 -1 O VAL B 93 N VAL A 9 SHEET 3 A 7 GLU B 66 LEU B 74 -1 N GLU B 68 O THR B 96 SHEET 4 A 7 LEU B 112 LEU B 120 -1 O LEU B 115 N TYR B 71 SHEET 5 A 7 ALA B 44 LEU B 52 -1 N MET B 50 O PHE B 114 SHEET 6 A 7 GLU B 28 HIS B 33 -1 N GLU B 30 O LYS B 51 SHEET 7 A 7 GLU B 17 SER B 20 -1 N GLU B 17 O MET B 31 SHEET 1 B 7 GLU A 17 SER A 20 0 SHEET 2 B 7 GLU A 28 HIS A 33 -1 O MET A 31 N GLU A 17 SHEET 3 B 7 ALA A 44 LEU A 52 -1 O ARG A 49 N ALA A 32 SHEET 4 B 7 LEU A 112 LEU A 120 -1 O PHE A 114 N MET A 50 SHEET 5 B 7 GLU A 66 LEU A 74 -1 N PHE A 67 O ILE A 119 SHEET 6 B 7 ASP A 92 THR A 96 -1 O THR A 96 N GLU A 68 SHEET 7 B 7 VAL B 8 ARG B 10 -1 O VAL B 9 N VAL A 93 SHEET 1 C 4 SER A 57 LYS A 62 0 SHEET 2 C 4 SER A 101 GLU A 105 -1 O ILE A 104 N VAL A 58 SHEET 3 C 4 GLU A 76 ASP A 81 -1 N VAL A 78 O GLU A 105 SHEET 4 C 4 LYS A 84 LYS A 89 -1 O VAL A 86 N PHE A 79 SHEET 1 D 4 SER B 57 LYS B 62 0 SHEET 2 D 4 SER B 101 GLU B 105 -1 O HIS B 102 N HIS B 61 SHEET 3 D 4 GLU B 76 ASP B 81 -1 N HIS B 80 O SER B 103 SHEET 4 D 4 LYS B 84 LYS B 89 -1 O VAL B 86 N PHE B 79 LINK NE2 HIS A 61 MN MN A 300 1555 1555 2.16 LINK NE2 HIS A 63 MN MN A 300 1555 1555 2.02 LINK OE2 GLU A 68 MN MN A 300 1555 1555 2.10 LINK NE2 HIS A 102 MN MN A 300 1555 1555 2.16 LINK MN MN A 300 O4 OXL A 400 1555 1555 2.31 LINK MN MN A 300 O3 OXL A 400 1555 1555 2.09 LINK NE2 HIS B 61 MN MN B 301 1555 1555 2.12 LINK NE2 HIS B 63 MN MN B 301 1555 1555 2.05 LINK OE2 GLU B 68 MN MN B 301 1555 1555 2.13 LINK NE2 HIS B 102 MN MN B 301 1555 1555 2.23 LINK MN MN B 301 O3 OXL B 401 1555 1555 2.17 LINK MN MN B 301 O4 OXL B 401 1555 1555 2.09 SITE 1 AC1 5 HIS A 61 HIS A 63 GLU A 68 HIS A 102 SITE 2 AC1 5 OXL A 400 SITE 1 AC2 5 HIS B 61 HIS B 63 GLU B 68 HIS B 102 SITE 2 AC2 5 OXL B 401 SITE 1 AC3 7 HIS A 61 HIS A 63 GLU A 68 TYR A 70 SITE 2 AC3 7 HIS A 102 MN A 300 HOH A 491 SITE 1 AC4 9 ARG B 23 HIS B 61 HIS B 63 GLU B 68 SITE 2 AC4 9 TYR B 70 HIS B 102 ILE B 118 MN B 301 SITE 3 AC4 9 HOH B 506 CRYST1 89.132 49.738 69.547 90.00 123.73 90.00 C 1 2 1 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 0.011219 0.000000 0.007491 0.00000 SCALE2 0.000000 0.020105 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017289 0.00000