HEADER OXIDOREDUCTASE 18-JAN-16 5HN3 TITLE CRYSTAL STRUCTURE OF BETA-DECARBOXYLATING DEHYDROGENASE (TK0280) FROM TITLE 2 THERMOCOCCUS KODAKARENSIS (APO FORM) 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 5HN3 1 REMARK REVDAT 3 19-FEB-20 5HN3 1 REMARK REVDAT 2 04-JAN-17 5HN3 1 JRNL REVDAT 1 07-DEC-16 5HN3 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 49108 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) : 0.200 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2647 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3594 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE SET COUNT : 183 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2544 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.160 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2595 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2542 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3509 ; 1.540 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5808 ; 0.876 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 6.530 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;31.319 ;22.605 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 431 ;14.138 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.236 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 398 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2962 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 600 ; 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): 1327 ; 2.177 ; 2.937 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1326 ; 2.177 ; 2.935 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1657 ; 3.137 ; 4.399 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1658 ; 3.137 ; 4.402 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1268 ; 2.598 ; 3.345 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1269 ; 2.597 ; 3.346 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1853 ; 4.049 ; 4.869 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3028 ; 5.855 ;24.036 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3029 ; 5.854 ;24.042 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 5HN3 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_1000217350. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-7.0 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-NW12A 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 : 52021 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 88.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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: 1X0L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, IMIDAZOLE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.05100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.72350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 87.99500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.05100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.72350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 87.99500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.05100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.72350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 87.99500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.05100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.72350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 87.99500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 53860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 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 91.44700 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 91.44700 REMARK 350 BIOMT3 4 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 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: 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 502 O HOH A 685 2.01 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 706 O HOH A 711 2565 2.15 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 LEU A 117 -47.79 -149.23 REMARK 500 SER A 156 -152.82 -123.93 REMARK 500 ALA A 253 53.86 37.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 125 ASN A 126 -140.53 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 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 248 O REMARK 620 2 VAL A 249 O 88.8 REMARK 620 3 HIS A 250 O 93.6 72.7 REMARK 620 4 HOH A 543 O 91.5 176.8 110.5 REMARK 620 5 HOH A 597 O 98.0 90.6 159.5 86.2 REMARK 620 6 HOH A 686 O 167.5 82.6 92.4 96.6 73.2 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 IMD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HN6 RELATED DB: PDB REMARK 900 RELATED ID: 5HN5 RELATED DB: PDB REMARK 900 RELATED ID: 5HN4 RELATED DB: PDB DBREF 5HN3 A 1 347 UNP Q5JFV8 Q5JFV8_THEKO 1 347 SEQADV 5HN3 HIS A 348 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN3 HIS A 349 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN3 HIS A 350 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN3 HIS A 351 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN3 HIS A 352 UNP Q5JFV8 EXPRESSION TAG SEQADV 5HN3 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 IMD A 401 5 HET IMD A 402 5 HET NA A 403 1 HETNAM IMD IMIDAZOLE HETNAM NA SODIUM ION FORMUL 2 IMD 2(C3 H5 N2 1+) FORMUL 4 NA NA 1+ FORMUL 5 HOH *220(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 SER A 61 1 11 HELIX 4 AA4 SER A 80 LEU A 89 1 10 HELIX 5 AA5 THR A 136 GLY A 155 1 20 HELIX 6 AA6 LEU A 167 GLY A 185 1 19 HELIX 7 AA7 ILE A 193 ASN A 203 1 11 HELIX 8 AA8 GLU A 213 ALA A 224 1 12 HELIX 9 AA9 THR A 225 ALA A 228 5 4 HELIX 10 AB1 SER A 230 ILE A 233 5 4 HELIX 11 AB2 ALA A 253 ALA A 257 5 5 HELIX 12 AB3 PRO A 264 LEU A 278 1 15 HELIX 13 AB4 ASP A 281 GLY A 296 1 16 HELIX 14 AB5 THR A 299 GLY A 303 5 5 HELIX 15 AB6 ARG A 307 MET A 325 1 19 SHEET 1 AA110 VAL A 31 TYR A 35 0 SHEET 2 AA110 TYR A 2 GLY A 9 1 N VAL A 6 O GLU A 34 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 VAL A 64 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 LEU A 211 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 PHE A 160 SHEET 1 AA2 2 TYR A 118 PHE A 119 0 SHEET 2 AA2 2 LEU A 134 ILE A 135 -1 O LEU A 134 N PHE A 119 SHEET 1 AA3 2 GLY A 122 VAL A 125 0 SHEET 2 AA3 2 ARG A 128 ASP A 131 -1 O VAL A 130 N ALA A 123 LINK O PRO A 248 NA NA A 403 1555 1555 2.39 LINK O VAL A 249 NA NA A 403 1555 1555 2.81 LINK O HIS A 250 NA NA A 403 1555 1555 2.25 LINK NA NA A 403 O HOH A 543 1555 1555 2.26 LINK NA NA A 403 O HOH A 597 1555 1555 2.43 LINK NA NA A 403 O HOH A 686 1555 1555 2.51 SITE 1 AC1 4 TYR A 118 ARG A 133 GLU A 213 HOH A 598 SITE 1 AC2 6 GLY A 104 GLU A 106 LEU A 269 ARG A 286 SITE 2 AC2 6 ARG A 290 HOH A 595 SITE 1 AC3 6 PRO A 248 VAL A 249 HIS A 250 HOH A 543 SITE 2 AC3 6 HOH A 597 HOH A 686 CRYST1 58.102 91.447 175.990 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017211 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005682 0.00000