HEADER OXIDOREDUCTASE 18-JAN-16 5HN5
TITLE CRYSTAL STRUCTURE OF BETA-DECARBOXYLATING DEHYDROGENASE (TK0280) FROM
TITLE 2 THERMOCOCCUS KODAKARENSIS COMPLEXED WITH MN AND ISOCITRATE
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 5HN5 1 LINK
REVDAT 3 19-FEB-20 5HN5 1 REMARK
REVDAT 2 04-JAN-17 5HN5 1 JRNL
REVDAT 1 07-DEC-16 5HN5 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. 2.55 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) : 2.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 141.06
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 14808
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) : 0.200
REMARK 3 R VALUE (WORKING SET) : 0.197
REMARK 3 FREE R VALUE : 0.257
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 778
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) : 2.55
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1076
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.43
REMARK 3 BIN R VALUE (WORKING SET) : 0.2510
REMARK 3 BIN FREE R VALUE SET COUNT : 54
REMARK 3 BIN FREE R VALUE : 0.3020
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2495
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 22
REMARK 3 SOLVENT ATOMS : 13
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.12
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.01000
REMARK 3 B22 (A**2) : -0.01000
REMARK 3 B33 (A**2) : 0.01000
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): 0.380
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.277
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.197
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.910
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2562 ; 0.009 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 2513 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3469 ; 1.440 ; 1.982
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5745 ; 0.887 ; 3.001
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 6.666 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;35.327 ;22.672
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 424 ;17.843 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;19.152 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 397 ; 0.088 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2926 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 579 ; 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): 1312 ; 3.917 ; 6.378
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1311 ; 3.918 ; 6.374
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1640 ; 5.664 ; 9.568
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1641 ; 5.663 ; 9.572
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1250 ; 4.592 ; 6.851
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1251 ; 4.590 ; 6.851
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1830 ; 6.934 ;10.074
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2854 ; 8.839 ;50.524
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2855 ; 8.837 ;50.530
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 5HN5 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_1000217352.
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 : 15751
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550
REMARK 200 RESOLUTION RANGE LOW (A) : 141.060
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 7.700
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 41.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.70
REMARK 200 R MERGE FOR SHELL (I) : 0.54400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300
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 (%): 58.28
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, 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 70.53150
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 105.79725
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 35.26575
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 70.53150
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 35.26575
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 105.79725
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: 5980 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 24920 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 -80.37200
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
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 VAL A 328
REMARK 465 TRP A 329
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. = 4.1 DEGREES
REMARK 500 ARG A 133 NE - CZ - NH2 ANGL. DEV. = -4.2 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 40.78 -106.81
REMARK 500 SER A 80 131.29 -38.56
REMARK 500 GLU A 115 -145.18 -142.26
REMARK 500 VAL A 125 115.70 -166.15
REMARK 500 GLU A 183 -38.47 -39.61
REMARK 500 HIS A 250 174.68 -56.42
REMARK 500 ALA A 253 59.09 36.81
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 53.8
REMARK 620 3 ICT A 401 O1 52.7 3.1
REMARK 620 4 ICT A 401 O7 59.3 5.5 6.9
REMARK 620 5 HOH A 504 O 52.8 7.7 4.7 9.6
REMARK 620 6 HOH A 510 O 57.9 9.6 7.7 8.3 5.2
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 ICT 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: 5HN6 RELATED DB: PDB
REMARK 900 RELATED ID: 5HN4 RELATED DB: PDB
REMARK 900 RELATED ID: 5HN3 RELATED DB: PDB
DBREF 5HN5 A 1 347 UNP Q5JFV8 Q5JFV8_THEKO 1 347
SEQADV 5HN5 HIS A 348 UNP Q5JFV8 EXPRESSION TAG
SEQADV 5HN5 HIS A 349 UNP Q5JFV8 EXPRESSION TAG
SEQADV 5HN5 HIS A 350 UNP Q5JFV8 EXPRESSION TAG
SEQADV 5HN5 HIS A 351 UNP Q5JFV8 EXPRESSION TAG
SEQADV 5HN5 HIS A 352 UNP Q5JFV8 EXPRESSION TAG
SEQADV 5HN5 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 ICT A 401 13
HET MN A 402 1
HET MPD A 403 8
HETNAM ICT ISOCITRIC ACID
HETNAM MN MANGANESE (II) ION
HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL
FORMUL 2 ICT C6 H8 O7
FORMUL 3 MN MN 2+
FORMUL 4 MPD C6 H14 O2
FORMUL 5 HOH *13(H2 O)
HELIX 1 AA1 ILE A 12 ALA A 26 1 15
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 GLY A 155 1 20
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 PRO A 204 HIS A 207 5 4
HELIX 10 AB1 GLU A 213 THR A 225 1 13
HELIX 11 AB2 VAL A 226 GLY A 229 5 4
HELIX 12 AB3 SER A 230 ILE A 233 5 4
HELIX 13 AB4 ALA A 253 ALA A 257 5 5
HELIX 14 AB5 PRO A 264 GLY A 279 1 16
HELIX 15 AB6 GLY A 282 VAL A 294 1 13
HELIX 16 AB7 THR A 299 GLY A 303 5 5
HELIX 17 AB8 ARG A 307 LEU A 323 1 17
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 ILE A 7
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 ILE A 109 N ARG A 96
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 VAL A 161 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 5455 2.08
LINK OD1 ASP A 218 MN MN A 402 1555 1555 2.06
LINK O1 ICT A 401 MN MN A 402 1555 1555 2.19
LINK O7 ICT A 401 MN MN A 402 1555 1555 2.24
LINK MN MN A 402 O HOH A 504 1555 1555 2.08
LINK MN MN A 402 O HOH A 510 1555 1555 2.30
SITE 1 AC1 11 SER A 80 ARG A 86 ARG A 96 ARG A 111
SITE 2 AC1 11 TYR A 118 LYS A 163 ASP A 194 ASP A 218
SITE 3 AC1 11 MN A 402 HOH A 502 HOH A 504
SITE 1 AC2 5 ASP A 194 ASP A 218 ICT A 401 HOH A 504
SITE 2 AC2 5 HOH A 510
SITE 1 AC3 6 ILE A 12 SER A 230 HIS A 250 ALA A 262
SITE 2 AC3 6 ASN A 263 ASP A 301
CRYST1 80.372 80.372 141.063 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 0.012442 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012442 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007089 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
