HEADER HYDROLASE 16-SEP-98 8PRK TITLE THE R78K AND D117E ACTIVE SITE VARIANTS OF SACCHAROMYCES CEREVISIAE TITLE 2 SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL STUDIES AND MECHANISTIC TITLE 3 IMPLICATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (INORGANIC PYROPHOSPHATASE); COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PPASE; COMPND 5 EC: 3.6.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 GENE: PPA1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HB101 KEYWDS ENZYME MECHANISM, IORGANIC PYROPHOSPHATASE, MUTANT STRUCTURES, 2- KEYWDS 2 METAL ION MECHANISM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.TUOMINEN,P.HEIKINHEIMO,T.KAJANDER,T.TORKKEL,T.HYYTIA,J.KAPYLA, AUTHOR 2 R.LAHTI,B.S.COOPERMAN,A.GOLDMAN REVDAT 6 20-SEP-23 8PRK 1 REMARK REVDAT 5 03-NOV-21 8PRK 1 REMARK SEQADV LINK REVDAT 4 24-FEB-09 8PRK 1 VERSN REVDAT 3 01-APR-03 8PRK 1 JRNL REVDAT 2 22-DEC-99 8PRK 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 23-DEC-98 8PRK 0 JRNL AUTH V.TUOMINEN,P.HEIKINHEIMO,T.KAJANDER,T.TORKKEL,T.HYYTIA, JRNL AUTH 2 J.KAPYLA,R.LAHTI,B.S.COOPERMAN,A.GOLDMAN JRNL TITL THE R78K AND D117E ACTIVE-SITE VARIANTS OF SACCHAROMYCES JRNL TITL 2 CEREVISIAE SOLUBLE INORGANIC PYROPHOSPHATASE: STRUCTURAL JRNL TITL 3 STUDIES AND MECHANISTIC IMPLICATIONS. JRNL REF J.MOL.BIOL. V. 284 1565 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9878371 JRNL DOI 10.1006/JMBI.1998.2266 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.HEIKINHEIMO,J.LEHTONEN,A.BAYKOV,R.LAHTI,B.S.COOPERMAN, REMARK 1 AUTH 2 A.GOLDMAN REMARK 1 TITL THE STRUCTURAL BASIS FOR PYROPHOSPHATASE CATALYSIS REMARK 1 REF STRUCTURE V. 4 1491 1996 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.HEIKINHEIMO,P.POHJANJOKI,A.HELMINEN,M.TASANEN, REMARK 1 AUTH 2 B.S.COOPERMAN,A.GOLDMAN,A.BAYKOV,R.LAHTI REMARK 1 TITL A SITE-DIRECTED MUTAGENESIS STUDY OF SACCHAROMYCES REMARK 1 TITL 2 CEREVISIAE PYROPHOSPHATASE FUNCTIONAL CONSERVATION OF THE REMARK 1 TITL 3 ACTIVE SITE OF SOLUBLE INORGANIC PYROPHOSPHATASES REMARK 1 REF EUR.J.BIOCHEM. V. 239 138 1996 REMARK 1 REFN ISSN 0014-2956 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 85.2 REMARK 3 NUMBER OF REFLECTIONS : 51133 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) : 0.190 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 4376 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2177 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 182 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4435 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 352 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.00 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.370 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) : 1.230 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.050 ; 2.500 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 : NULL REMARK 3 PARAMETER FILE 2 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 3 : PARAMETER.ELEMENTS REMARK 3 PARAMETER FILE 4 : PARAM11.WAT REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPPO4.PR REMARK 3 TOPOLOGY FILE 3 : TOPH11.WAT REMARK 3 TOPOLOGY FILE 4 : TOPOLOGY.ELEMENTS REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 8PRK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008081. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.891 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54387 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1WGJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17-19 % MPD 25 MM MES, PH 6.0 1 MM REMARK 280 MNCL2 0.5 MM NA2HPO4 10 MG/ML PROTEIN 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 29.35000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.35000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.15000 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 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 0 REMARK 465 SER A 283 REMARK 465 GLY A 284 REMARK 465 SER A 285 REMARK 465 VAL A 286 REMARK 465 MET B 1000 REMARK 465 SER B 1283 REMARK 465 GLY B 1284 REMARK 465 SER B 1285 REMARK 465 VAL B 1286 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 THR A 1 OG1 CG2 REMARK 470 LYS A 24 CG CD CE NZ REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 ASN A 169 CG OD1 ND2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 ASP A 249 CG OD1 OD2 REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 LYS A 274 CG CD CE NZ REMARK 470 LYS B1038 CG CD CE NZ REMARK 470 GLU B1039 CG CD OE1 OE2 REMARK 470 ASN B1040 CG OD1 ND2 REMARK 470 GLU B1062 CG CD OE1 OE2 REMARK 470 LYS B1111 CG CD CE NZ REMARK 470 GLN B1202 CG CD OE1 NE2 REMARK 470 GLU B1221 CG CD OE1 OE2 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 236 103.52 -161.96 REMARK 500 SER A 265 52.25 -146.40 REMARK 500 LYS A 278 128.06 -38.62 REMARK 500 ASN B1066 57.74 39.96 REMARK 500 ASP B1236 108.83 -164.82 REMARK 500 SER B1254 93.08 -161.92 REMARK 500 SER B1265 56.37 -140.56 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 A2001 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 115 OD2 REMARK 620 2 ASP A 120 OD2 164.4 REMARK 620 3 ASP A 152 OD1 90.6 73.8 REMARK 620 4 PO4 A3002 O2 99.9 83.5 95.9 REMARK 620 5 PO4 A3002 O4 83.2 111.5 154.9 61.6 REMARK 620 6 HOH A4001 O 90.2 90.0 96.4 164.0 108.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A2002 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 120 OD1 REMARK 620 2 PO4 A3002 O4 100.0 REMARK 620 3 PO4 A3002 O1 99.4 62.3 REMARK 620 4 HOH A4002 O 171.4 87.1 88.1 REMARK 620 5 HOH A4003 O 80.6 170.5 108.2 93.2 REMARK 620 6 HOH A4004 O 81.3 93.5 155.7 93.6 95.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A2004 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 147 OD2 REMARK 620 2 ASP A 152 OD2 101.5 REMARK 620 3 PO4 A3002 O2 160.7 91.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B2005 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B1115 OD2 REMARK 620 2 ASP B1120 OD2 162.8 REMARK 620 3 ASP B1152 OD1 93.0 72.4 REMARK 620 4 PO4 B3004 O4 84.7 112.1 160.5 REMARK 620 5 PO4 B3004 O1 106.8 85.5 102.1 60.6 REMARK 620 6 HOH B4008 O 85.4 86.3 92.8 106.2 160.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B2006 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B1120 OD1 REMARK 620 2 PO4 B3004 O4 98.8 REMARK 620 3 PO4 B3004 O3 99.0 67.3 REMARK 620 4 HOH B4009 O 82.3 92.6 159.8 REMARK 620 5 HOH B4010 O 164.6 96.1 90.3 93.3 REMARK 620 6 HOH B4011 O 80.2 168.5 101.4 98.7 85.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B2008 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B1147 OD2 REMARK 620 2 ASP B1152 OD2 97.6 REMARK 620 3 PO4 B3004 O1 157.3 100.3 REMARK 620 4 HOH B4012 O 81.1 177.2 81.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: MN1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: METAL 1 BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: MN2 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: METAL 2 BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: MN4 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: METAL 4 BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 2005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 2004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 2008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 2006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 3004 DBREF 8PRK A 0 286 UNP P00817 IPYR_YEAST 1 287 DBREF 8PRK B 1000 1286 UNP P00817 IPYR_YEAST 1 287 SEQADV 8PRK LYS A 78 UNP P00817 ARG 79 ENGINEERED MUTATION SEQADV 8PRK LYS B 1078 UNP P00817 ARG 79 ENGINEERED MUTATION SEQRES 1 A 287 MET THR TYR THR THR ARG GLN ILE GLY ALA LYS ASN THR SEQRES 2 A 287 LEU GLU TYR LYS VAL TYR ILE GLU LYS ASP GLY LYS PRO SEQRES 3 A 287 VAL SER ALA PHE HIS ASP ILE PRO LEU TYR ALA ASP LYS SEQRES 4 A 287 GLU ASN ASN ILE PHE ASN MET VAL VAL GLU ILE PRO ARG SEQRES 5 A 287 TRP THR ASN ALA LYS LEU GLU ILE THR LYS GLU GLU THR SEQRES 6 A 287 LEU ASN PRO ILE ILE GLN ASP THR LYS LYS GLY LYS LEU SEQRES 7 A 287 LYS PHE VAL ARG ASN CYS PHE PRO HIS HIS GLY TYR ILE SEQRES 8 A 287 HIS ASN TYR GLY ALA PHE PRO GLN THR TRP GLU ASP PRO SEQRES 9 A 287 ASN VAL SER HIS PRO GLU THR LYS ALA VAL GLY ASP ASN SEQRES 10 A 287 ASP PRO ILE ASP VAL LEU GLU ILE GLY GLU THR ILE ALA SEQRES 11 A 287 TYR THR GLY GLN VAL LYS GLN VAL LYS ALA LEU GLY ILE SEQRES 12 A 287 MET ALA LEU LEU ASP GLU GLY GLU THR ASP TRP LYS VAL SEQRES 13 A 287 ILE ALA ILE ASP ILE ASN ASP PRO LEU ALA PRO LYS LEU SEQRES 14 A 287 ASN ASP ILE GLU ASP VAL GLU LYS TYR PHE PRO GLY LEU SEQRES 15 A 287 LEU ARG ALA THR ASN GLU TRP PHE ARG ILE TYR LYS ILE SEQRES 16 A 287 PRO ASP GLY LYS PRO GLU ASN GLN PHE ALA PHE SER GLY SEQRES 17 A 287 GLU ALA LYS ASN LYS LYS TYR ALA LEU ASP ILE ILE LYS SEQRES 18 A 287 GLU THR HIS ASP SER TRP LYS GLN LEU ILE ALA GLY LYS SEQRES 19 A 287 SER SER ASP SER LYS GLY ILE ASP LEU THR ASN VAL THR SEQRES 20 A 287 LEU PRO ASP THR PRO THR TYR SER LYS ALA ALA SER ASP SEQRES 21 A 287 ALA ILE PRO PRO ALA SER LEU LYS ALA ASP ALA PRO ILE SEQRES 22 A 287 ASP LYS SER ILE ASP LYS TRP PHE PHE ILE SER GLY SER SEQRES 23 A 287 VAL SEQRES 1 B 287 MET THR TYR THR THR ARG GLN ILE GLY ALA LYS ASN THR SEQRES 2 B 287 LEU GLU TYR LYS VAL TYR ILE GLU LYS ASP GLY LYS PRO SEQRES 3 B 287 VAL SER ALA PHE HIS ASP ILE PRO LEU TYR ALA ASP LYS SEQRES 4 B 287 GLU ASN ASN ILE PHE ASN MET VAL VAL GLU ILE PRO ARG SEQRES 5 B 287 TRP THR ASN ALA LYS LEU GLU ILE THR LYS GLU GLU THR SEQRES 6 B 287 LEU ASN PRO ILE ILE GLN ASP THR LYS LYS GLY LYS LEU SEQRES 7 B 287 LYS PHE VAL ARG ASN CYS PHE PRO HIS HIS GLY TYR ILE SEQRES 8 B 287 HIS ASN TYR GLY ALA PHE PRO GLN THR TRP GLU ASP PRO SEQRES 9 B 287 ASN VAL SER HIS PRO GLU THR LYS ALA VAL GLY ASP ASN SEQRES 10 B 287 ASP PRO ILE ASP VAL LEU GLU ILE GLY GLU THR ILE ALA SEQRES 11 B 287 TYR THR GLY GLN VAL LYS GLN VAL LYS ALA LEU GLY ILE SEQRES 12 B 287 MET ALA LEU LEU ASP GLU GLY GLU THR ASP TRP LYS VAL SEQRES 13 B 287 ILE ALA ILE ASP ILE ASN ASP PRO LEU ALA PRO LYS LEU SEQRES 14 B 287 ASN ASP ILE GLU ASP VAL GLU LYS TYR PHE PRO GLY LEU SEQRES 15 B 287 LEU ARG ALA THR ASN GLU TRP PHE ARG ILE TYR LYS ILE SEQRES 16 B 287 PRO ASP GLY LYS PRO GLU ASN GLN PHE ALA PHE SER GLY SEQRES 17 B 287 GLU ALA LYS ASN LYS LYS TYR ALA LEU ASP ILE ILE LYS SEQRES 18 B 287 GLU THR HIS ASP SER TRP LYS GLN LEU ILE ALA GLY LYS SEQRES 19 B 287 SER SER ASP SER LYS GLY ILE ASP LEU THR ASN VAL THR SEQRES 20 B 287 LEU PRO ASP THR PRO THR TYR SER LYS ALA ALA SER ASP SEQRES 21 B 287 ALA ILE PRO PRO ALA SER LEU LYS ALA ASP ALA PRO ILE SEQRES 22 B 287 ASP LYS SER ILE ASP LYS TRP PHE PHE ILE SER GLY SER SEQRES 23 B 287 VAL HET MN A2004 1 HET MN A2002 1 HET MN A2001 1 HET PO4 A3002 5 HET MN B2005 1 HET MN B2008 1 HET MN B2006 1 HET PO4 B3004 5 HETNAM MN MANGANESE (II) ION HETNAM PO4 PHOSPHATE ION FORMUL 3 MN 6(MN 2+) FORMUL 6 PO4 2(O4 P 3-) FORMUL 11 HOH *352(H2 O) HELIX 1 1 LYS A 38 ASN A 40 5 3 HELIX 2 2 ALA A 165 LYS A 167 5 3 HELIX 3 3 ILE A 171 TYR A 177 1 7 HELIX 4 4 LEU A 181 ILE A 191 1 11 HELIX 5 5 ILE A 194 ASP A 196 5 3 HELIX 6 6 ALA A 204 GLY A 207 5 4 HELIX 7 7 LYS A 212 ILE A 230 1 19 HELIX 8 8 LYS A 274 ASP A 277 1 4 HELIX 9 9 ALA B 1165 LYS B 1167 5 3 HELIX 10 10 ILE B 1171 TYR B 1177 5 7 HELIX 11 11 LEU B 1181 ILE B 1191 1 11 HELIX 12 12 ILE B 1194 ASP B 1196 5 3 HELIX 13 13 ALA B 1204 GLY B 1207 5 4 HELIX 14 14 LYS B 1212 ILE B 1230 1 19 HELIX 15 15 LYS B 1255 ASP B 1259 5 5 HELIX 16 16 LYS B 1274 ASP B 1277 5 4 SHEET 1 A 3 TYR A 2 ILE A 7 0 SHEET 2 A 3 LYS A 16 LYS A 21 -1 N GLU A 20 O THR A 3 SHEET 3 A 3 LYS A 24 VAL A 26 -1 N VAL A 26 O ILE A 19 SHEET 1 B 7 VAL A 134 LYS A 138 0 SHEET 2 B 7 ILE A 42 ILE A 49 -1 N MET A 45 O LYS A 135 SHEET 3 B 7 ASN A 92 PHE A 96 -1 N ALA A 95 O VAL A 46 SHEET 4 B 7 ASP A 120 GLU A 123 -1 N GLU A 123 O ASN A 92 SHEET 5 B 7 GLU A 150 ASP A 159 1 N VAL A 155 O ASP A 120 SHEET 6 B 7 VAL A 137 ASP A 147 -1 N ASP A 147 O GLU A 150 SHEET 7 B 7 ALA A 209 ASN A 211 -1 N LYS A 210 O ILE A 142 SHEET 1 C 2 LEU A 57 ILE A 59 0 SHEET 2 C 2 ILE A 68 GLN A 70 -1 N ILE A 69 O GLU A 58 SHEET 1 D 4 SER B1265 LYS B1267 0 SHEET 2 D 4 TYR B1002 ALA B1009 1 N GLY B1008 O SER B1265 SHEET 3 D 4 LYS B1016 LYS B1021 -1 N GLU B1020 O THR B1003 SHEET 4 D 4 LYS B1024 VAL B1026 -1 N VAL B1026 O ILE B1019 SHEET 1 E 7 VAL B1134 LYS B1138 0 SHEET 2 E 7 ILE B1042 ILE B1049 -1 N MET B1045 O LYS B1135 SHEET 3 E 7 ASN B1092 PHE B1096 -1 N ALA B1095 O VAL B1046 SHEET 4 E 7 ASP B1120 GLU B1123 -1 N GLU B1123 O ASN B1092 SHEET 5 E 7 LYS B1154 ASP B1159 1 N VAL B1155 O ASP B1120 SHEET 6 E 7 VAL B1137 MET B1143 -1 N MET B1143 O LYS B1154 SHEET 7 E 7 ALA B1209 ASN B1211 -1 N LYS B1210 O ILE B1142 SHEET 1 F 2 LEU B1057 ILE B1059 0 SHEET 2 F 2 ILE B1068 GLN B1070 -1 N ILE B1069 O GLU B1058 LINK OD2 ASP A 115 MN MN A2001 1555 1555 2.42 LINK OD2 ASP A 120 MN MN A2001 1555 1555 2.37 LINK OD1 ASP A 120 MN MN A2002 1555 1555 2.35 LINK OD2 ASP A 147 MN MN A2004 1555 1555 2.35 LINK OD1 ASP A 152 MN MN A2001 1555 1555 2.31 LINK OD2 ASP A 152 MN MN A2004 1555 1555 2.36 LINK MN MN A2001 O2 PO4 A3002 1555 1555 2.38 LINK MN MN A2001 O4 PO4 A3002 1555 1555 2.53 LINK MN MN A2001 O HOH A4001 1555 1555 2.45 LINK MN MN A2002 O4 PO4 A3002 1555 1555 2.51 LINK MN MN A2002 O1 PO4 A3002 1555 1555 2.53 LINK MN MN A2002 O HOH A4002 1555 1555 2.53 LINK MN MN A2002 O HOH A4003 1555 1555 2.42 LINK MN MN A2002 O HOH A4004 1555 1555 2.42 LINK MN MN A2004 O2 PO4 A3002 1555 1555 2.35 LINK OD2 ASP B1115 MN MN B2005 1555 1555 2.37 LINK OD2 ASP B1120 MN MN B2005 1555 1555 2.44 LINK OD1 ASP B1120 MN MN B2006 1555 1555 2.33 LINK OD2 ASP B1147 MN MN B2008 1555 1555 2.39 LINK OD1 ASP B1152 MN MN B2005 1555 1555 2.34 LINK OD2 ASP B1152 MN MN B2008 1555 1555 2.37 LINK MN MN B2005 O4 PO4 B3004 1555 1555 2.41 LINK MN MN B2005 O1 PO4 B3004 1555 1555 2.46 LINK MN MN B2005 O HOH B4008 1555 1555 2.44 LINK MN MN B2006 O4 PO4 B3004 1555 1555 2.47 LINK MN MN B2006 O3 PO4 B3004 1555 1555 2.48 LINK MN MN B2006 O HOH B4009 1555 1555 2.46 LINK MN MN B2006 O HOH B4010 1555 1555 2.42 LINK MN MN B2006 O HOH B4011 1555 1555 2.38 LINK MN MN B2008 O1 PO4 B3004 1555 1555 2.37 LINK MN MN B2008 O HOH B4012 1555 1555 2.48 CISPEP 1 PHE A 84 PRO A 85 0 0.29 CISPEP 2 PHE B 1084 PRO B 1085 0 0.21 SITE 1 MN1 4 ASP A 117 ASP A 152 ASP A 115 ASP A 120 SITE 1 MN2 3 ASP A 117 TYR A 93 ASP A 120 SITE 1 MN4 2 ASP A 152 ASP A 147 SITE 1 AC1 6 ASP B1115 ASP B1120 ASP B1152 MN B2008 SITE 2 AC1 6 PO4 B3004 HOH B4008 SITE 1 AC2 3 ASP A 147 ASP A 152 PO4 A3002 SITE 1 AC3 5 ASP B1147 ASP B1152 MN B2005 PO4 B3004 SITE 2 AC3 5 HOH B4012 SITE 1 AC4 5 ASP B1120 PO4 B3004 HOH B4009 HOH B4010 SITE 2 AC4 5 HOH B4011 SITE 1 AC5 5 ASP A 120 PO4 A3002 HOH A4002 HOH A4003 SITE 2 AC5 5 HOH A4004 SITE 1 AC6 5 ASP A 115 ASP A 120 ASP A 152 PO4 A3002 SITE 2 AC6 5 HOH A4001 SITE 1 AC7 12 LYS A 56 TYR A 93 ASP A 115 ASP A 117 SITE 2 AC7 12 ASP A 120 ASP A 152 LYS A 154 MN A2001 SITE 3 AC7 12 MN A2002 MN A2004 HOH A4021 HOH A4262 SITE 1 AC8 12 LYS B1056 TYR B1093 ASP B1115 ASP B1117 SITE 2 AC8 12 ASP B1120 ASP B1152 LYS B1154 MN B2005 SITE 3 AC8 12 MN B2006 MN B2008 HOH B4012 HOH B4202 CRYST1 58.700 102.300 117.000 90.00 90.00 90.00 P 21 21 21 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 0.017036 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008547 0.00000 MTRIX1 1 0.799085 0.601106 0.011616 34.79830 1 MTRIX2 1 0.601138 -0.799145 0.000919 -102.66670 1 MTRIX3 1 0.009835 0.006248 -0.999932 -90.46280 1