HEADER OXIDOREDUCTASE 18-JAN-16 5HN6 TITLE CRYSTAL STRUCTURE OF BETA-DECARBOXYLATING DEHYDROGENASE (TK0280) FROM TITLE 2 THERMOCOCCUS KODAKARENSIS COMPLEXED WITH MN AND 3-ISOPROPYLMALATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMOISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 SOURCE 3 / JCM 12380 / KOD1); SOURCE 4 ORGANISM_TAXID: 69014; SOURCE 5 STRAIN: ATCC BAA-918 / JCM 12380 / KOD1; SOURCE 6 GENE: TK0280; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 CODONPLUS (RIL) KEYWDS HOMOISOCITRATE DEHYDROGENASE, BETA-DECARBOXYLATING DEHYDROGENASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SHIMIZU,T.TOMITA,M.NISHIYAMA REVDAT 4 08-NOV-23 5HN6 1 LINK REVDAT 3 19-FEB-20 5HN6 1 REMARK REVDAT 2 04-JAN-17 5HN6 1 JRNL REVDAT 1 07-DEC-16 5HN6 0 JRNL AUTH T.SHIMIZU,L.YIN,A.YOSHIDA,Y.YOKOOJI,S.I.HACHISUKA,T.SATO, JRNL AUTH 2 T.TOMITA,H.NISHIDA,H.ATOMI,T.KUZUYAMA,M.NISHIYAMA JRNL TITL STRUCTURE AND FUNCTION OF AN ANCESTRAL-TYPE JRNL TITL 2 BETA-DECARBOXYLATING DEHYDROGENASE FROM THERMOCOCCUS JRNL TITL 3 KODAKARENSIS JRNL REF BIOCHEM. J. V. 474 105 2017 JRNL REFN ESSN 1470-8728 JRNL PMID 27831491 JRNL DOI 10.1042/BCJ20160699 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 142.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 15853 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 832 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1137 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2516 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.342 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.257 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.195 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.757 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2575 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2531 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3487 ; 1.537 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5783 ; 0.863 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 7.167 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;34.273 ;22.586 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;17.197 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;17.038 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 400 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2926 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 583 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1315 ; 4.470 ; 6.243 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1314 ; 4.462 ; 6.241 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1642 ; 6.198 ; 9.364 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1643 ; 6.197 ; 9.368 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1260 ; 5.015 ; 6.695 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1261 ; 5.013 ; 6.695 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1846 ; 7.329 ; 9.848 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2921 ; 9.149 ;49.706 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2922 ; 9.148 ;49.713 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5HN6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000217353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16850 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 142.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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: 5HN4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, SODIUM CHLORIDE, 2-METHYL-2,4 REMARK 280 -PENTANEDIOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 71.44500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.16750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.72250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 71.44500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 35.72250 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 107.16750 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: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 285.78000 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 ARG A 330 REMARK 465 ASP A 331 REMARK 465 GLU A 332 REMARK 465 ILE A 333 REMARK 465 ARG A 334 REMARK 465 LEU A 335 REMARK 465 SER A 336 REMARK 465 ARG A 337 REMARK 465 LEU A 338 REMARK 465 GLU A 339 REMARK 465 SER A 340 REMARK 465 ASP A 341 REMARK 465 ILE A 342 REMARK 465 SER A 343 REMARK 465 ARG A 344 REMARK 465 MET A 345 REMARK 465 ALA A 346 REMARK 465 GLY A 347 REMARK 465 HIS A 348 REMARK 465 HIS A 349 REMARK 465 HIS A 350 REMARK 465 HIS A 351 REMARK 465 HIS A 352 REMARK 465 HIS A 353 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 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 133 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ASP A 74 40.12 -103.57 REMARK 500 LEU A 101 45.79 -95.00 REMARK 500 ARG A 102 -58.52 -124.25 REMARK 500 GLU A 115 -139.44 -126.67 REMARK 500 SER A 156 -156.25 -134.05 REMARK 500 ALA A 253 60.87 26.96 REMARK 500 LEU A 280 -168.28 -102.27 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 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 194 OD2 REMARK 620 2 ASP A 218 OD1 55.6 REMARK 620 3 IPM A 401 O1 61.2 5.8 REMARK 620 4 IPM A 401 O3 54.4 2.4 6.8 REMARK 620 5 HOH A 504 O 57.8 9.3 8.5 7.7 REMARK 620 6 HOH A 508 O 53.1 7.2 9.7 4.9 5.1 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 IPM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HN5 RELATED DB: PDB REMARK 900 RELATED ID: 5HN4 RELATED DB: PDB REMARK 900 RELATED ID: 5HN3 RELATED DB: PDB REMARK 900 5HN3 IS THE APO FORM DBREF 5HN6 A 1 347 UNP Q5JFV8 Q5JFV8_THEKO 1 347 SEQADV 5HN6 HIS A 348 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN6 HIS A 349 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN6 HIS A 350 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN6 HIS A 351 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN6 HIS A 352 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN6 HIS A 353 UNP Q5JFV8 EXPRESSION TAG SEQRES 1 A 353 MET TYR ARG VAL ALA VAL ILE PRO GLY ASP GLY ILE GLY SEQRES 2 A 353 PRO GLU VAL ILE ASP GLY ALA VAL ARG VAL LEU LYS ALA SEQRES 3 A 353 VAL THR GLY ARG VAL ARG PHE GLU TYR TYR GLU GLY GLY SEQRES 4 A 353 VAL ASP VAL PHE GLN GLU CYS GLY SER PRO ILE ARG GLU SEQRES 5 A 353 GLU ASP LEU GLU GLU ILE ARG ARG SER ASP ALA VAL LEU SEQRES 6 A 353 PHE GLY ALA THR THR THR PRO PHE ASP LEU PRO GLY TYR SEQRES 7 A 353 ARG SER LEU ILE LEU THR LEU ARG LYS GLU LEU GLY LEU SEQRES 8 A 353 TYR ALA ASN LEU ARG ILE ILE PRO ASP LEU ARG THR GLY SEQRES 9 A 353 ARG GLU ILE VAL ILE VAL ARG GLU ASN SER GLU GLY LEU SEQRES 10 A 353 TYR PHE GLY ILE GLY ALA VAL VAL ASN GLY ARG ALA VAL SEQRES 11 A 353 ASP VAL ARG LEU ILE THR ARG GLU GLY ALA GLU ARG ILE SEQRES 12 A 353 ALA ARG PHE ALA VAL GLU GLN ALA LYS ALA ARG GLY SER SEQRES 13 A 353 PHE ILE THR PHE VAL HIS LYS ALA ASN VAL LEU THR GLY SEQRES 14 A 353 ASP LYS PHE PHE ARG ARG ILE VAL ARG GLU VAL ALA GLY SEQRES 15 A 353 GLU GLU GLY VAL GLU VAL ARG ASP ALA ILE ILE ASP SER SEQRES 16 A 353 PHE THR ILE LYS LEU VAL ARG ASN PRO TRP GLU HIS GLY SEQRES 17 A 353 VAL ILE LEU SER GLU ASN LEU PHE GLY ASP ILE LEU SER SEQRES 18 A 353 ASP LEU ALA THR VAL HIS ALA GLY SER ILE GLY ILE VAL SEQRES 19 A 353 PRO SER GLY ASN TYR GLY ASP GLY ILE ALA LEU PHE GLU SEQRES 20 A 353 PRO VAL HIS GLY SER ALA PRO ASP ILE ALA GLY LYS GLY SEQRES 21 A 353 ILE ALA ASN PRO ILE GLY ALA ILE LEU SER GLY ALA MET SEQRES 22 A 353 LEU LEU ASP TYR LEU GLY LEU ASP GLY SER LEU ILE ARG SEQRES 23 A 353 ALA ALA VAL ARG GLY TYR VAL VAL ASN GLY GLU LEU THR SEQRES 24 A 353 PRO ASP MET GLY GLY ARG ALA ARG THR GLU ASP VAL VAL SEQRES 25 A 353 ARG GLY ILE ILE GLY GLU ILE GLU ASP LEU LEU SER MET SEQRES 26 A 353 ASP GLU VAL TRP ARG ASP GLU ILE ARG LEU SER ARG LEU SEQRES 27 A 353 GLU SER ASP ILE SER ARG MET ALA GLY HIS HIS HIS HIS SEQRES 28 A 353 HIS HIS HET IPM A 401 12 HET MN A 402 1 HET MPD A 403 8 HETNAM IPM 3-ISOPROPYLMALIC ACID HETNAM MN MANGANESE (II) ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 IPM C7 H12 O5 FORMUL 3 MN MN 2+ FORMUL 4 MPD C6 H14 O2 FORMUL 5 HOH *19(H2 O) HELIX 1 AA1 ILE A 12 THR A 28 1 17 HELIX 2 AA2 GLY A 39 GLY A 47 1 9 HELIX 3 AA3 ARG A 51 ARG A 59 1 9 HELIX 4 AA4 SER A 80 LEU A 89 1 10 HELIX 5 AA5 GLU A 115 PHE A 119 5 5 HELIX 6 AA6 THR A 136 ALA A 153 1 18 HELIX 7 AA7 LEU A 167 GLU A 184 1 18 HELIX 8 AA8 ILE A 193 ASN A 203 1 11 HELIX 9 AA9 GLU A 213 ALA A 224 1 12 HELIX 10 AB1 THR A 225 HIS A 227 5 3 HELIX 11 AB2 SER A 230 ILE A 233 5 4 HELIX 12 AB3 PRO A 264 GLY A 279 1 16 HELIX 13 AB4 GLY A 282 GLY A 296 1 15 HELIX 14 AB5 ARG A 307 SER A 324 1 18 SHEET 1 AA110 VAL A 31 TYR A 35 0 SHEET 2 AA110 TYR A 2 GLY A 9 1 N TYR A 2 O ARG A 32 SHEET 3 AA110 ALA A 63 ALA A 68 1 O LEU A 65 N ALA A 5 SHEET 4 AA110 ALA A 244 PRO A 248 1 O PHE A 246 N PHE A 66 SHEET 5 AA110 PRO A 235 TYR A 239 -1 N ASN A 238 O LEU A 245 SHEET 6 AA110 ALA A 93 PRO A 99 -1 N ALA A 93 O TYR A 239 SHEET 7 AA110 GLU A 106 GLU A 112 -1 O ARG A 111 N ASN A 94 SHEET 8 AA110 VAL A 209 SER A 212 1 O ILE A 210 N VAL A 110 SHEET 9 AA110 ILE A 158 HIS A 162 1 N THR A 159 O LEU A 211 SHEET 10 AA110 VAL A 188 ILE A 192 1 O ARG A 189 N ILE A 158 SHEET 1 AA2 2 GLY A 122 VAL A 124 0 SHEET 2 AA2 2 ALA A 129 ASP A 131 -1 O VAL A 130 N ALA A 123 LINK OD2 ASP A 194 MN MN A 402 1555 5557 1.96 LINK OD1 ASP A 218 MN MN A 402 1555 1555 1.98 LINK O1 IPM A 401 MN MN A 402 1555 1555 2.37 LINK O3 IPM A 401 MN MN A 402 1555 1555 2.04 LINK MN MN A 402 O HOH A 504 1555 1555 2.15 LINK MN MN A 402 O HOH A 508 1555 1555 2.12 SITE 1 AC1 11 ARG A 86 ARG A 96 ARG A 111 TYR A 118 SITE 2 AC1 11 LYS A 163 ASP A 194 ASP A 218 MN A 402 SITE 3 AC1 11 HOH A 501 HOH A 504 HOH A 508 SITE 1 AC2 5 ASP A 194 ASP A 218 IPM A 401 HOH A 504 SITE 2 AC2 5 HOH A 508 SITE 1 AC3 6 ILE A 12 HIS A 250 ILE A 256 ALA A 262 SITE 2 AC3 6 ASN A 263 ASP A 301 CRYST1 80.161 80.161 142.890 90.00 90.00 90.00 P 43 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 0.012475 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012475 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006998 0.00000