HEADER METAL BINDING PROTEIN 30-JUN-09 3A44 TITLE CRYSTAL STRUCTURE OF HYPA IN THE DIMERIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE NICKEL INCORPORATION PROTEIN HYPA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: HYPA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS KODAKARAENSIS; SOURCE 3 ORGANISM_COMMON: THERMOCOCCUS KODAKARAENSIS; SOURCE 4 ORGANISM_TAXID: 69014; SOURCE 5 STRAIN: KOD1; SOURCE 6 GENE: HYPA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21(+)A KEYWDS [NIFE] HYDROGENASE MATURATION, ZINC-FINGER, NICKEL BINDING, DOMAIN KEYWDS 2 SWAPPING, METAL-BINDING, NICKEL, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WATANABE,T.ARAI,R.MATSUMI,H.ATOMI,T.IMANAKA,K.MIKI REVDAT 4 01-NOV-23 3A44 1 REMARK LINK REVDAT 3 11-DEC-19 3A44 1 SSBOND LINK REVDAT 2 22-FEB-17 3A44 1 JRNL VERSN REVDAT 1 06-OCT-09 3A44 0 JRNL AUTH S.WATANABE,T.ARAI,R.MATSUMI,H.ATOMI,T.IMANAKA,K.MIKI JRNL TITL CRYSTAL STRUCTURE OF HYPA, A NICKEL-BINDING METALLOCHAPERONE JRNL TITL 2 FOR [NIFE] HYDROGENASE MATURATION. JRNL REF J.MOL.BIOL. V. 394 448 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19769985 JRNL DOI 10.1016/J.JMB.2009.09.030 REMARK 2 REMARK 2 RESOLUTION. 3.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1639961.110 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 10976 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 SET) : 0.292 REMARK 3 FREE R VALUE : 0.337 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 539 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1135 REMARK 3 BIN R VALUE (WORKING SET) : 0.4200 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 58 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3848 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 125.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : 46.80000 REMARK 3 B33 (A**2) : -46.58000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.58 REMARK 3 ESD FROM SIGMAA (A) : 0.98 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.63 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.64 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 62.38 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3A44 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000028786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 LIQUID NITROGEN COOLING 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 : 11039 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09200 REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45400 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3A43 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, PH8.5, 24% PEG8000, 22% REMARK 280 ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.41500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.24000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.98750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.24000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.41500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.98750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 6530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -129.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 5520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -124.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 FME A 1 REMARK 465 SER A 139 REMARK 465 PHE B 99 REMARK 465 ILE B 100 REMARK 465 PRO B 101 REMARK 465 GLU B 102 REMARK 465 GLY B 137 REMARK 465 GLY B 138 REMARK 465 SER B 139 REMARK 465 FME C 1 REMARK 465 ASP C 90 REMARK 465 GLU C 91 REMARK 465 ARG C 92 REMARK 465 ILE C 93 REMARK 465 LYS C 94 REMARK 465 GLU C 95 REMARK 465 ASP C 96 REMARK 465 ILE C 97 REMARK 465 HIS C 98 REMARK 465 PHE C 99 REMARK 465 ILE C 100 REMARK 465 PRO C 101 REMARK 465 GLU C 102 REMARK 465 VAL C 103 REMARK 465 GLY C 138 REMARK 465 SER C 139 REMARK 465 FME D 1 REMARK 465 HIS D 2 REMARK 465 LYS D 94 REMARK 465 GLU D 95 REMARK 465 ASP D 96 REMARK 465 ILE D 97 REMARK 465 HIS D 98 REMARK 465 PHE D 99 REMARK 465 ILE D 100 REMARK 465 PRO D 101 REMARK 465 GLY D 138 REMARK 465 SER D 139 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 HIS A 2 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 3 CG CD OE1 OE2 REMARK 470 TRP A 4 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 4 CZ3 CH2 REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 VAL A 85 CG1 CG2 REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 PHE A 89 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 91 CG CD OE1 OE2 REMARK 470 ARG A 92 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 HIS A 98 CG ND1 CD2 CE1 NE2 REMARK 470 HIS A 105 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 108 CG CD1 CD2 REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 GLU A 136 CG CD OE1 OE2 REMARK 470 LEU B 51 CG CD1 CD2 REMARK 470 GLU B 61 CG CD OE1 OE2 REMARK 470 GLU B 68 CG CD OE1 OE2 REMARK 470 LYS B 86 CG CD CE NZ REMARK 470 LYS B 88 CG CD CE NZ REMARK 470 ASP B 90 CG OD1 OD2 REMARK 470 LYS B 94 CG CD CE NZ REMARK 470 ASP B 96 CG OD1 OD2 REMARK 470 ILE B 97 CG1 CG2 CD1 REMARK 470 HIS B 98 CG ND1 CD2 CE1 NE2 REMARK 470 VAL B 103 CG1 CG2 REMARK 470 VAL B 104 CG1 CG2 REMARK 470 LYS B 112 CG CD CE NZ REMARK 470 ARG B 124 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 136 CG CD OE1 OE2 REMARK 470 TRP C 4 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP C 4 CZ3 CH2 REMARK 470 GLU C 61 CG CD OE1 OE2 REMARK 470 LYS C 83 CG CD CE NZ REMARK 470 LYS C 86 CG CD CE NZ REMARK 470 ASP C 87 CG OD1 OD2 REMARK 470 LYS C 88 CG CD CE NZ REMARK 470 PHE C 89 CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL C 104 CG1 CG2 REMARK 470 HIS C 105 CG ND1 CD2 CE1 NE2 REMARK 470 PHE C 107 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU C 108 CG CD1 CD2 REMARK 470 LYS C 112 CG CD CE NZ REMARK 470 ARG C 124 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 136 CG CD OE1 OE2 REMARK 470 GLU D 61 CG CD OE1 OE2 REMARK 470 ARG D 74 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 83 CG CD CE NZ REMARK 470 VAL D 85 CG1 CG2 REMARK 470 ASP D 87 CG OD1 OD2 REMARK 470 LYS D 88 CG CD CE NZ REMARK 470 PHE D 89 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP D 90 CG OD1 OD2 REMARK 470 GLU D 91 CG CD OE1 OE2 REMARK 470 ARG D 92 CG CD NE CZ NH1 NH2 REMARK 470 ILE D 93 CG1 CG2 CD1 REMARK 470 GLU D 102 CG CD OE1 OE2 REMARK 470 VAL D 103 CG1 CG2 REMARK 470 LEU D 108 CG CD1 CD2 REMARK 470 ARG D 124 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 136 CB CG CD OE1 OE2 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 PRO C 111 C - N - CA ANGL. DEV. = 10.9 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 GLU A 68 164.57 -45.06 REMARK 500 ASN A 75 -38.20 -154.19 REMARK 500 LYS A 83 -6.59 -57.91 REMARK 500 ASP A 96 145.61 -37.21 REMARK 500 HIS A 98 -2.45 -58.49 REMARK 500 PHE A 99 -70.86 -74.31 REMARK 500 CYS A 113 -66.04 -127.07 REMARK 500 SER A 115 -168.16 36.90 REMARK 500 HIS A 116 0.60 -176.47 REMARK 500 VAL A 121 -81.85 -94.11 REMARK 500 ALA B 5 -32.85 -39.72 REMARK 500 ARG B 25 143.56 179.51 REMARK 500 GLU B 35 4.86 -64.38 REMARK 500 ILE B 56 2.26 -68.19 REMARK 500 ASN B 77 -4.01 81.33 REMARK 500 LYS B 112 -73.75 -59.38 REMARK 500 SER B 115 -120.66 48.67 REMARK 500 HIS B 116 -2.47 98.64 REMARK 500 VAL B 126 89.71 -151.10 REMARK 500 TYR B 127 -166.09 -118.12 REMARK 500 ARG C 20 24.45 -70.66 REMARK 500 ARG C 25 148.95 -173.59 REMARK 500 ASN C 77 37.97 35.02 REMARK 500 LEU C 82 16.52 -62.43 REMARK 500 HIS C 105 43.05 -79.63 REMARK 500 ALA C 106 89.78 -68.01 REMARK 500 CYS C 110 78.12 3.84 REMARK 500 PRO C 111 11.26 -55.53 REMARK 500 SER C 115 -164.49 36.03 REMARK 500 HIS C 116 -1.03 179.21 REMARK 500 LYS D 27 -76.41 -99.48 REMARK 500 GLU D 68 166.58 -31.32 REMARK 500 ASN D 77 -9.78 89.97 REMARK 500 CYS D 113 -150.40 -98.36 REMARK 500 SER D 115 -127.65 54.72 REMARK 500 HIS D 116 1.14 103.51 REMARK 500 VAL D 121 -82.34 -106.39 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 ZN A 140 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 73 SG REMARK 620 2 CYS A 76 SG 110.0 REMARK 620 3 CYS B 110 SG 109.3 113.9 REMARK 620 4 CYS B 113 SG 101.1 109.3 112.4 REMARK 620 5 SER B 115 OG 63.2 162.6 83.4 59.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 140 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 110 SG REMARK 620 2 CYS A 113 SG 107.5 REMARK 620 3 CYS B 73 SG 109.1 108.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 140 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 73 SG REMARK 620 2 CYS C 76 SG 108.3 REMARK 620 3 CYS D 110 SG 109.2 109.0 REMARK 620 4 CYS D 113 SG 109.0 109.9 111.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 141 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 110 SG REMARK 620 2 CYS C 113 SG 111.4 REMARK 620 3 CYS D 73 SG 101.8 129.5 REMARK 620 4 CYS D 76 SG 116.1 87.5 111.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 140 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 140 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 140 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 141 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A43 RELATED DB: PDB DBREF 3A44 A 1 139 UNP Q5JIH3 HYPA_PYRKO 1 139 DBREF 3A44 B 1 139 UNP Q5JIH3 HYPA_PYRKO 1 139 DBREF 3A44 C 1 139 UNP Q5JIH3 HYPA_PYRKO 1 139 DBREF 3A44 D 1 139 UNP Q5JIH3 HYPA_PYRKO 1 139 SEQRES 1 A 139 FME HIS GLU TRP ALA LEU ALA ASP ALA ILE VAL ARG THR SEQRES 2 A 139 VAL LEU ASP TYR ALA GLN ARG GLU GLY ALA SER ARG VAL SEQRES 3 A 139 LYS ALA VAL ARG VAL VAL LEU GLY GLU LEU GLN ASP VAL SEQRES 4 A 139 ALA GLU ASP ILE VAL LYS PHE ALA MET GLU GLN LEU PHE SEQRES 5 A 139 ALA GLY THR ILE ALA GLU GLY ALA GLU ILE GLU PHE VAL SEQRES 6 A 139 GLU GLU GLU ALA VAL PHE LYS CYS ARG ASN CYS ASN TYR SEQRES 7 A 139 GLU TRP LYS LEU LYS GLU VAL LYS ASP LYS PHE ASP GLU SEQRES 8 A 139 ARG ILE LYS GLU ASP ILE HIS PHE ILE PRO GLU VAL VAL SEQRES 9 A 139 HIS ALA PHE LEU ALA CYS PRO LYS CYS GLY SER HIS ASP SEQRES 10 A 139 PHE GLU VAL VAL LYS GLY ARG GLY VAL TYR VAL ALA GLY SEQRES 11 A 139 ILE LYS ILE GLU LYS GLU GLY GLY SER SEQRES 1 B 139 FME HIS GLU TRP ALA LEU ALA ASP ALA ILE VAL ARG THR SEQRES 2 B 139 VAL LEU ASP TYR ALA GLN ARG GLU GLY ALA SER ARG VAL SEQRES 3 B 139 LYS ALA VAL ARG VAL VAL LEU GLY GLU LEU GLN ASP VAL SEQRES 4 B 139 ALA GLU ASP ILE VAL LYS PHE ALA MET GLU GLN LEU PHE SEQRES 5 B 139 ALA GLY THR ILE ALA GLU GLY ALA GLU ILE GLU PHE VAL SEQRES 6 B 139 GLU GLU GLU ALA VAL PHE LYS CYS ARG ASN CYS ASN TYR SEQRES 7 B 139 GLU TRP LYS LEU LYS GLU VAL LYS ASP LYS PHE ASP GLU SEQRES 8 B 139 ARG ILE LYS GLU ASP ILE HIS PHE ILE PRO GLU VAL VAL SEQRES 9 B 139 HIS ALA PHE LEU ALA CYS PRO LYS CYS GLY SER HIS ASP SEQRES 10 B 139 PHE GLU VAL VAL LYS GLY ARG GLY VAL TYR VAL ALA GLY SEQRES 11 B 139 ILE LYS ILE GLU LYS GLU GLY GLY SER SEQRES 1 C 139 FME HIS GLU TRP ALA LEU ALA ASP ALA ILE VAL ARG THR SEQRES 2 C 139 VAL LEU ASP TYR ALA GLN ARG GLU GLY ALA SER ARG VAL SEQRES 3 C 139 LYS ALA VAL ARG VAL VAL LEU GLY GLU LEU GLN ASP VAL SEQRES 4 C 139 ALA GLU ASP ILE VAL LYS PHE ALA MET GLU GLN LEU PHE SEQRES 5 C 139 ALA GLY THR ILE ALA GLU GLY ALA GLU ILE GLU PHE VAL SEQRES 6 C 139 GLU GLU GLU ALA VAL PHE LYS CYS ARG ASN CYS ASN TYR SEQRES 7 C 139 GLU TRP LYS LEU LYS GLU VAL LYS ASP LYS PHE ASP GLU SEQRES 8 C 139 ARG ILE LYS GLU ASP ILE HIS PHE ILE PRO GLU VAL VAL SEQRES 9 C 139 HIS ALA PHE LEU ALA CYS PRO LYS CYS GLY SER HIS ASP SEQRES 10 C 139 PHE GLU VAL VAL LYS GLY ARG GLY VAL TYR VAL ALA GLY SEQRES 11 C 139 ILE LYS ILE GLU LYS GLU GLY GLY SER SEQRES 1 D 139 FME HIS GLU TRP ALA LEU ALA ASP ALA ILE VAL ARG THR SEQRES 2 D 139 VAL LEU ASP TYR ALA GLN ARG GLU GLY ALA SER ARG VAL SEQRES 3 D 139 LYS ALA VAL ARG VAL VAL LEU GLY GLU LEU GLN ASP VAL SEQRES 4 D 139 ALA GLU ASP ILE VAL LYS PHE ALA MET GLU GLN LEU PHE SEQRES 5 D 139 ALA GLY THR ILE ALA GLU GLY ALA GLU ILE GLU PHE VAL SEQRES 6 D 139 GLU GLU GLU ALA VAL PHE LYS CYS ARG ASN CYS ASN TYR SEQRES 7 D 139 GLU TRP LYS LEU LYS GLU VAL LYS ASP LYS PHE ASP GLU SEQRES 8 D 139 ARG ILE LYS GLU ASP ILE HIS PHE ILE PRO GLU VAL VAL SEQRES 9 D 139 HIS ALA PHE LEU ALA CYS PRO LYS CYS GLY SER HIS ASP SEQRES 10 D 139 PHE GLU VAL VAL LYS GLY ARG GLY VAL TYR VAL ALA GLY SEQRES 11 D 139 ILE LYS ILE GLU LYS GLU GLY GLY SER MODRES 3A44 FME B 1 MET N-FORMYLMETHIONINE HET FME B 1 10 HET ZN A 140 1 HET ZN B 140 1 HET ZN C 140 1 HET ZN C 141 1 HETNAM FME N-FORMYLMETHIONINE HETNAM ZN ZINC ION FORMUL 2 FME C6 H11 N O3 S FORMUL 5 ZN 4(ZN 2+) HELIX 1 1 HIS A 2 ARG A 20 1 19 HELIX 2 2 ALA A 40 ALA A 53 1 14 HELIX 3 3 LEU A 82 LYS A 94 1 13 HELIX 4 4 HIS A 98 LEU A 108 1 11 HELIX 5 5 TRP B 4 ARG B 20 1 17 HELIX 6 6 ALA B 40 ALA B 53 1 14 HELIX 7 7 LEU B 82 GLU B 91 1 10 HELIX 8 8 VAL B 103 LEU B 108 1 6 HELIX 9 9 HIS C 2 ARG C 20 1 19 HELIX 10 10 ALA C 40 ALA C 53 1 14 HELIX 11 11 LYS C 83 PHE C 89 1 7 HELIX 12 12 TRP D 4 ARG D 20 1 17 HELIX 13 13 ALA D 40 ALA D 53 1 14 HELIX 14 14 LEU D 82 LYS D 86 1 5 HELIX 15 15 ASP D 87 ILE D 93 1 7 HELIX 16 16 VAL D 104 LEU D 108 5 5 SHEET 1 A 3 GLU A 61 GLU A 67 0 SHEET 2 A 3 ARG A 25 GLY A 34 1 N VAL A 31 O VAL A 65 SHEET 3 A 3 VAL B 126 GLU B 134 -1 O LYS B 132 N LYS A 27 SHEET 1 B 3 GLU A 79 LYS A 81 0 SHEET 2 B 3 VAL A 70 LYS A 72 -1 N PHE A 71 O TRP A 80 SHEET 3 B 3 VAL B 120 LYS B 122 -1 O LYS B 122 N VAL A 70 SHEET 1 C 3 PHE A 118 LYS A 122 0 SHEET 2 C 3 VAL B 70 CYS B 73 -1 O LYS B 72 N GLU A 119 SHEET 3 C 3 GLU B 79 LYS B 81 -1 O TRP B 80 N PHE B 71 SHEET 1 D 3 VAL A 126 GLU A 134 0 SHEET 2 D 3 ARG B 25 GLY B 34 -1 O ARG B 30 N GLY A 130 SHEET 3 D 3 GLU B 61 GLU B 67 1 O VAL B 65 N LEU B 33 SHEET 1 E 3 GLU C 61 GLU C 67 0 SHEET 2 E 3 ARG C 25 GLY C 34 1 N LEU C 33 O GLU C 67 SHEET 3 E 3 VAL D 126 GLU D 134 -1 O GLY D 130 N ARG C 30 SHEET 1 F 3 GLU C 79 LYS C 81 0 SHEET 2 F 3 VAL C 70 CYS C 73 -1 N PHE C 71 O TRP C 80 SHEET 3 F 3 PHE D 118 VAL D 120 -1 O GLU D 119 N LYS C 72 SHEET 1 G 3 GLU C 119 LYS C 122 0 SHEET 2 G 3 VAL D 70 LYS D 72 -1 O VAL D 70 N LYS C 122 SHEET 3 G 3 GLU D 79 LYS D 81 -1 O TRP D 80 N PHE D 71 SHEET 1 H 3 VAL C 126 GLU C 134 0 SHEET 2 H 3 ARG D 25 GLY D 34 -1 O VAL D 32 N TYR C 127 SHEET 3 H 3 GLU D 61 GLU D 67 1 O VAL D 65 N VAL D 31 LINK C FME B 1 N HIS B 2 1555 1555 1.33 LINK SG CYS A 73 ZN ZN A 140 1555 1555 2.23 LINK SG CYS A 76 ZN ZN A 140 1555 1555 2.10 LINK SG CYS A 110 ZN ZN B 140 1555 1555 2.23 LINK SG CYS A 113 ZN ZN B 140 1555 1555 2.71 LINK ZN ZN A 140 SG CYS B 110 1555 1555 2.17 LINK ZN ZN A 140 SG CYS B 113 1555 1555 2.33 LINK ZN ZN A 140 OG SER B 115 1555 1555 2.49 LINK SG CYS B 73 ZN ZN B 140 1555 1555 2.22 LINK SG CYS C 73 ZN ZN C 140 1555 1555 2.44 LINK SG CYS C 76 ZN ZN C 140 1555 1555 2.09 LINK SG CYS C 110 ZN ZN C 141 1555 1555 2.14 LINK SG CYS C 113 ZN ZN C 141 1555 1555 2.53 LINK ZN ZN C 140 SG CYS D 110 1555 1555 2.24 LINK ZN ZN C 140 SG CYS D 113 1555 1555 2.28 LINK ZN ZN C 141 SG CYS D 73 1555 1555 2.47 LINK ZN ZN C 141 SG CYS D 76 1555 1555 2.03 SITE 1 AC1 5 CYS A 73 CYS A 76 CYS B 110 CYS B 113 SITE 2 AC1 5 SER B 115 SITE 1 AC2 4 CYS A 110 CYS A 113 CYS B 73 CYS B 76 SITE 1 AC3 4 CYS C 73 CYS C 76 CYS D 110 CYS D 113 SITE 1 AC4 5 CYS C 110 CYS C 113 SER C 115 CYS D 73 SITE 2 AC4 5 CYS D 76 CRYST1 56.830 97.975 136.480 90.00 90.00 90.00 P 21 21 21 16 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 0.017596 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007327 0.00000