HEADER BIOSYNTHETIC PROTEIN 02-FEB-09 3G3R TITLE CRYSTAL STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX TITLE 2 WITH APPNHP-MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR TRANSPORTER CHAPERONE 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 189-480; COMPND 5 SYNONYM: PHOSPHATE METABOLISM PROTEIN 3; COMPND 6 ENGINEERED: 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 GENE: J1345, PHM3, VTC4, YJL012C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM11 KEYWDS POLYPHOSPHATE POLYMERASE, POLYPHOSPHATE KINASE, VTC COMPLEX, VACUOLAR KEYWDS 2 TRANSPORTER CHAPERONE, TUNNEL ENZYME, MEMBRANE, PHOSPHOPROTEIN, KEYWDS 3 TRANSMEMBRANE, VACUOLE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.HOTHORN REVDAT 2 06-SEP-23 3G3R 1 REMARK SEQADV LINK REVDAT 1 05-MAY-09 3G3R 0 JRNL AUTH M.HOTHORN,H.NEUMANN,E.D.LENHERR,M.WEHNER,V.RYBIN,P.O.HASSA, JRNL AUTH 2 A.UTTENWEILER,M.REINHARDT,A.SCHMIDT,J.SEILER,A.G.LADURNER, JRNL AUTH 3 C.HERRMANN,K.SCHEFFZEK,A.MAYER JRNL TITL CATALYTIC CORE OF A MEMBRANE-ASSOCIATED EUKARYOTIC JRNL TITL 2 POLYPHOSPHATE POLYMERASE. JRNL REF SCIENCE V. 324 513 2009 JRNL REFN ISSN 0036-8075 JRNL PMID 19390046 JRNL DOI 10.1126/SCIENCE.1168120 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.700 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 46801 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2340 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.9084 - 6.1524 0.90 2594 171 0.2078 0.2285 REMARK 3 2 6.1524 - 4.9074 0.93 2671 189 0.2043 0.2191 REMARK 3 3 4.9074 - 4.2942 0.92 2736 86 0.1597 0.1838 REMARK 3 4 4.2942 - 3.9048 0.93 2723 157 0.1720 0.1826 REMARK 3 5 3.9048 - 3.6267 0.94 2750 134 0.1787 0.2242 REMARK 3 6 3.6267 - 3.4140 0.95 2788 148 0.1798 0.1823 REMARK 3 7 3.4140 - 3.2438 0.96 2789 158 0.1979 0.2291 REMARK 3 8 3.2438 - 3.1031 0.97 2861 130 0.2100 0.2905 REMARK 3 9 3.1031 - 2.9841 0.97 2852 152 0.2134 0.2839 REMARK 3 10 2.9841 - 2.8814 0.98 2837 181 0.2158 0.2596 REMARK 3 11 2.8814 - 2.7916 0.98 2858 155 0.2083 0.2727 REMARK 3 12 2.7916 - 2.7120 0.98 2854 151 0.2071 0.2716 REMARK 3 13 2.7120 - 2.6407 0.97 2861 159 0.2184 0.2662 REMARK 3 14 2.6407 - 2.5765 0.98 2875 136 0.2146 0.3459 REMARK 3 15 2.5765 - 2.5180 0.98 2829 161 0.2107 0.2390 REMARK 3 16 2.5180 - 2.4645 0.98 2894 139 0.2152 0.2503 REMARK 3 17 2.4645 - 2.4153 0.98 2851 168 0.2174 0.2505 REMARK 3 18 2.4153 - 2.3698 0.98 2897 148 0.2183 0.2721 REMARK 3 19 2.3698 - 2.3275 0.98 2859 153 0.2284 0.2579 REMARK 3 20 2.3275 - 2.2881 0.97 2828 162 0.2308 0.3103 REMARK 3 21 2.2881 - 2.2513 0.97 2827 149 0.2309 0.2881 REMARK 3 22 2.2513 - 2.2167 0.97 2822 147 0.2539 0.3424 REMARK 3 23 2.2167 - 2.1841 0.98 2869 166 0.2486 0.3279 REMARK 3 24 2.1841 - 2.1534 0.97 2810 154 0.2522 0.3036 REMARK 3 25 2.1534 - 2.1243 0.97 2857 145 0.2704 0.2914 REMARK 3 26 2.1243 - 2.0968 0.97 2844 140 0.2572 0.2786 REMARK 3 27 2.0968 - 2.0706 0.97 2830 151 0.2700 0.3112 REMARK 3 28 2.0706 - 2.0457 0.97 2846 152 0.2804 0.3668 REMARK 3 29 2.0457 - 2.0219 0.97 2802 151 0.2920 0.3662 REMARK 3 30 2.0219 - 2.0000 0.94 2764 144 0.2945 0.3913 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 51.45 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 NULL REMARK 3 ANGLE : 1.000 NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3G3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051385. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.970 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 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: PDB ENTRY 3G3Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M REMARK 280 BIS-TRIS, 10% JEFFAMINE M-600, PH 5.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K 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 34.13000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.18500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.48500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.18500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.13000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.48500 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 186 REMARK 465 ALA A 187 REMARK 465 MET A 188 REMARK 465 GLY A 189 REMARK 465 LYS A 190 REMARK 465 GLN A 191 REMARK 465 GLN A 192 REMARK 465 ASN A 193 REMARK 465 PHE A 194 REMARK 465 GLY B 186 REMARK 465 ALA B 187 REMARK 465 MET B 188 REMARK 465 GLY B 189 REMARK 465 LYS B 190 REMARK 465 GLN B 191 REMARK 465 GLN B 192 REMARK 465 LYS B 228 REMARK 465 GLU B 229 REMARK 465 GLN B 480 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 TRP A 287 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 287 CZ3 CH2 REMARK 470 LEU A 366 CG CD1 CD2 REMARK 470 ARG A 371 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 432 CG CD OE1 NE2 REMARK 470 LEU A 433 CG CD1 CD2 REMARK 470 GLU A 436 CG CD OE1 OE2 REMARK 470 GLU A 443 CG CD OE1 OE2 REMARK 470 ASN B 193 CG OD1 ND2 REMARK 470 PHE B 194 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 196 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 227 CG OD1 ND2 REMARK 470 ASP B 286 CG OD1 OD2 REMARK 470 LYS B 396 CG CD CE NZ REMARK 470 GLN B 432 CG CD OE1 NE2 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 VAL A 354 -51.04 -125.60 REMARK 500 GLN A 365 125.13 -170.42 REMARK 500 LEU A 467 43.46 -109.31 REMARK 500 LEU B 216 2.38 -67.56 REMARK 500 HIS B 218 -34.31 -138.63 REMARK 500 LYS B 326 -79.47 -67.02 REMARK 500 VAL B 354 -50.28 -129.34 REMARK 500 PRO B 367 135.06 -39.69 REMARK 500 TRP B 477 -4.93 -57.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ANP A 1000 REMARK 610 ANP B 1000 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 A1001 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 426 OE1 REMARK 620 2 GLU A 426 OE2 53.3 REMARK 620 3 ANP A1000 O3G 155.5 103.5 REMARK 620 4 ANP A1000 O2B 100.3 85.6 83.8 REMARK 620 5 ANP A1000 O1A 93.5 141.5 111.1 81.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1001 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 174 O REMARK 620 2 GLU B 426 OE1 79.4 REMARK 620 3 GLU B 426 OE2 98.4 54.3 REMARK 620 4 ANP B1000 O1B 165.7 111.8 82.3 REMARK 620 5 ANP B1000 O1A 100.1 92.9 138.2 88.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP B 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3G3Q RELATED DB: PDB REMARK 900 EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH A PHOSPHATE REMARK 900 POLYMER REMARK 900 RELATED ID: 3G3O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTICALLY IMPAIRED SUBUNIT VTC2P THAT REMARK 900 IS PART OF THE SAME MEMBRANE-INTEGRAL PROTEIN COMPLEX REMARK 900 RELATED ID: 3G3T RELATED DB: PDB REMARK 900 STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH REMARK 900 ORTHOPHOSPHATE REMARK 900 RELATED ID: 3G3U RELATED DB: PDB REMARK 900 STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH REMARK 900 PYROPHOSPHATE DBREF 3G3R A 189 480 UNP P47075 VTC4_YEAST 189 480 DBREF 3G3R B 189 480 UNP P47075 VTC4_YEAST 189 480 SEQADV 3G3R GLY A 186 UNP P47075 EXPRESSION TAG SEQADV 3G3R ALA A 187 UNP P47075 EXPRESSION TAG SEQADV 3G3R MET A 188 UNP P47075 EXPRESSION TAG SEQADV 3G3R GLY B 186 UNP P47075 EXPRESSION TAG SEQADV 3G3R ALA B 187 UNP P47075 EXPRESSION TAG SEQADV 3G3R MET B 188 UNP P47075 EXPRESSION TAG SEQRES 1 A 295 GLY ALA MET GLY LYS GLN GLN ASN PHE VAL ARG GLN THR SEQRES 2 A 295 THR LYS TYR TRP VAL HIS PRO ASP ASN ILE THR GLU LEU SEQRES 3 A 295 LYS LEU ILE ILE LEU LYS HIS LEU PRO VAL LEU VAL PHE SEQRES 4 A 295 ASN THR ASN LYS GLU PHE GLU ARG GLU ASP SER ALA ILE SEQRES 5 A 295 THR SER ILE TYR PHE ASP ASN GLU ASN LEU ASP LEU TYR SEQRES 6 A 295 TYR GLY ARG LEU ARG LYS ASP GLU GLY ALA GLU ALA HIS SEQRES 7 A 295 ARG LEU ARG TRP TYR GLY GLY MET SER THR ASP THR ILE SEQRES 8 A 295 PHE VAL GLU ARG LYS THR HIS ARG GLU ASP TRP THR GLY SEQRES 9 A 295 GLU LYS SER VAL LYS ALA ARG PHE ALA LEU LYS GLU ARG SEQRES 10 A 295 HIS VAL ASN ASP PHE LEU LYS GLY LYS TYR THR VAL ASP SEQRES 11 A 295 GLN VAL PHE ALA LYS MET ARG LYS GLU GLY LYS LYS PRO SEQRES 12 A 295 MET ASN GLU ILE GLU ASN LEU GLU ALA LEU ALA SER GLU SEQRES 13 A 295 ILE GLN TYR VAL MET LEU LYS LYS LYS LEU ARG PRO VAL SEQRES 14 A 295 VAL ARG SER PHE TYR ASN ARG THR ALA PHE GLN LEU PRO SEQRES 15 A 295 GLY ASP ALA ARG VAL ARG ILE SER LEU ASP THR GLU LEU SEQRES 16 A 295 THR MET VAL ARG GLU ASP ASN PHE ASP GLY VAL ASP ARG SEQRES 17 A 295 THR HIS LYS ASN TRP ARG ARG THR ASP ILE GLY VAL ASP SEQRES 18 A 295 TRP PRO PHE LYS GLN LEU ASP ASP LYS ASP ILE CYS ARG SEQRES 19 A 295 PHE PRO TYR ALA VAL LEU GLU VAL LYS LEU GLN THR GLN SEQRES 20 A 295 LEU GLY GLN GLU PRO PRO GLU TRP VAL ARG GLU LEU VAL SEQRES 21 A 295 GLY SER HIS LEU VAL GLU PRO VAL PRO LYS PHE SER LYS SEQRES 22 A 295 PHE ILE HIS GLY VAL ALA THR LEU LEU ASN ASP LYS VAL SEQRES 23 A 295 ASP SER ILE PRO PHE TRP LEU PRO GLN SEQRES 1 B 295 GLY ALA MET GLY LYS GLN GLN ASN PHE VAL ARG GLN THR SEQRES 2 B 295 THR LYS TYR TRP VAL HIS PRO ASP ASN ILE THR GLU LEU SEQRES 3 B 295 LYS LEU ILE ILE LEU LYS HIS LEU PRO VAL LEU VAL PHE SEQRES 4 B 295 ASN THR ASN LYS GLU PHE GLU ARG GLU ASP SER ALA ILE SEQRES 5 B 295 THR SER ILE TYR PHE ASP ASN GLU ASN LEU ASP LEU TYR SEQRES 6 B 295 TYR GLY ARG LEU ARG LYS ASP GLU GLY ALA GLU ALA HIS SEQRES 7 B 295 ARG LEU ARG TRP TYR GLY GLY MET SER THR ASP THR ILE SEQRES 8 B 295 PHE VAL GLU ARG LYS THR HIS ARG GLU ASP TRP THR GLY SEQRES 9 B 295 GLU LYS SER VAL LYS ALA ARG PHE ALA LEU LYS GLU ARG SEQRES 10 B 295 HIS VAL ASN ASP PHE LEU LYS GLY LYS TYR THR VAL ASP SEQRES 11 B 295 GLN VAL PHE ALA LYS MET ARG LYS GLU GLY LYS LYS PRO SEQRES 12 B 295 MET ASN GLU ILE GLU ASN LEU GLU ALA LEU ALA SER GLU SEQRES 13 B 295 ILE GLN TYR VAL MET LEU LYS LYS LYS LEU ARG PRO VAL SEQRES 14 B 295 VAL ARG SER PHE TYR ASN ARG THR ALA PHE GLN LEU PRO SEQRES 15 B 295 GLY ASP ALA ARG VAL ARG ILE SER LEU ASP THR GLU LEU SEQRES 16 B 295 THR MET VAL ARG GLU ASP ASN PHE ASP GLY VAL ASP ARG SEQRES 17 B 295 THR HIS LYS ASN TRP ARG ARG THR ASP ILE GLY VAL ASP SEQRES 18 B 295 TRP PRO PHE LYS GLN LEU ASP ASP LYS ASP ILE CYS ARG SEQRES 19 B 295 PHE PRO TYR ALA VAL LEU GLU VAL LYS LEU GLN THR GLN SEQRES 20 B 295 LEU GLY GLN GLU PRO PRO GLU TRP VAL ARG GLU LEU VAL SEQRES 21 B 295 GLY SER HIS LEU VAL GLU PRO VAL PRO LYS PHE SER LYS SEQRES 22 B 295 PHE ILE HIS GLY VAL ALA THR LEU LEU ASN ASP LYS VAL SEQRES 23 B 295 ASP SER ILE PRO PHE TRP LEU PRO GLN HET ANP A1000 13 HET MN A1001 1 HET SO4 A 2 5 HET SO4 A 5 5 HET SO4 A 7 5 HET NA A 1 1 HET ANP B1000 13 HET MN B1001 1 HET SO4 B 3 5 HET SO4 B 4 5 HET SO4 B 6 5 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION FORMUL 3 ANP 2(C10 H17 N6 O12 P3) FORMUL 4 MN 2(MN 2+) FORMUL 5 SO4 6(O4 S 2-) FORMUL 8 NA NA 1+ FORMUL 14 HOH *338(H2 O) HELIX 1 1 ASN A 207 LYS A 217 1 11 HELIX 2 2 GLU A 231 ASP A 234 5 4 HELIX 3 3 LEU A 247 LYS A 256 1 10 HELIX 4 4 HIS A 303 LYS A 309 1 7 HELIX 5 5 THR A 313 GLY A 325 1 13 HELIX 6 6 PRO A 328 LYS A 349 1 22 HELIX 7 7 ASP A 413 LYS A 415 5 3 HELIX 8 8 PRO A 438 SER A 447 1 10 HELIX 9 9 SER A 457 LEU A 467 1 11 HELIX 10 10 HIS B 204 ASP B 206 5 3 HELIX 11 11 ASN B 207 LEU B 216 1 10 HELIX 12 12 LEU B 247 LYS B 256 1 10 HELIX 13 13 GLU B 285 GLY B 289 5 5 HELIX 14 14 HIS B 303 LYS B 309 1 7 HELIX 15 15 THR B 313 PHE B 318 1 6 HELIX 16 16 PHE B 318 GLU B 324 1 7 HELIX 17 17 PRO B 328 LYS B 349 1 22 HELIX 18 18 ASP B 413 LYS B 415 5 3 HELIX 19 19 PRO B 438 GLY B 446 1 9 HELIX 20 20 SER B 457 LEU B 467 1 11 SHEET 1 A 7 GLY A 289 LYS A 300 0 SHEET 2 A 7 THR A 275 ASP A 286 -1 N VAL A 278 O PHE A 297 SHEET 3 A 7 GLU A 261 TYR A 268 -1 N ARG A 264 O GLU A 279 SHEET 4 A 7 ALA A 236 ASP A 243 -1 N PHE A 242 O HIS A 263 SHEET 5 A 7 ARG A 352 LEU A 366 -1 O VAL A 355 N TYR A 241 SHEET 6 A 7 ASP A 369 ARG A 384 -1 O VAL A 383 N ARG A 356 SHEET 7 A 7 ILE A 417 ARG A 419 -1 O CYS A 418 N MET A 382 SHEET 1 B 9 GLY A 289 LYS A 300 0 SHEET 2 B 9 THR A 275 ASP A 286 -1 N VAL A 278 O PHE A 297 SHEET 3 B 9 GLU A 261 TYR A 268 -1 N ARG A 264 O GLU A 279 SHEET 4 B 9 ALA A 236 ASP A 243 -1 N PHE A 242 O HIS A 263 SHEET 5 B 9 ARG A 352 LEU A 366 -1 O VAL A 355 N TYR A 241 SHEET 6 B 9 ASP A 369 ARG A 384 -1 O VAL A 383 N ARG A 356 SHEET 7 B 9 ALA A 423 GLN A 430 -1 O LYS A 428 N ARG A 373 SHEET 8 B 9 ARG A 196 VAL A 203 -1 N GLN A 197 O LEU A 429 SHEET 9 B 9 GLU A 451 PRO A 452 -1 O GLU A 451 N TRP A 202 SHEET 1 C 2 VAL A 221 VAL A 223 0 SHEET 2 C 2 LEU B 222 PHE B 224 1 O VAL B 223 N VAL A 221 SHEET 1 D 7 VAL B 293 LYS B 300 0 SHEET 2 D 7 THR B 275 THR B 282 -1 N THR B 282 O VAL B 293 SHEET 3 D 7 GLU B 261 TYR B 268 -1 N ARG B 266 O PHE B 277 SHEET 4 D 7 ALA B 236 ASP B 243 -1 N ILE B 240 O LEU B 265 SHEET 5 D 7 ARG B 352 LEU B 366 -1 O VAL B 355 N TYR B 241 SHEET 6 D 7 ASP B 369 ARG B 384 -1 O THR B 381 N PHE B 358 SHEET 7 D 7 ILE B 417 ARG B 419 -1 O CYS B 418 N MET B 382 SHEET 1 E 9 VAL B 293 LYS B 300 0 SHEET 2 E 9 THR B 275 THR B 282 -1 N THR B 282 O VAL B 293 SHEET 3 E 9 GLU B 261 TYR B 268 -1 N ARG B 266 O PHE B 277 SHEET 4 E 9 ALA B 236 ASP B 243 -1 N ILE B 240 O LEU B 265 SHEET 5 E 9 ARG B 352 LEU B 366 -1 O VAL B 355 N TYR B 241 SHEET 6 E 9 ASP B 369 ARG B 384 -1 O THR B 381 N PHE B 358 SHEET 7 E 9 ALA B 423 GLN B 432 -1 O LYS B 428 N ARG B 373 SHEET 8 E 9 PHE B 194 VAL B 203 -1 N VAL B 195 O THR B 431 SHEET 9 E 9 GLU B 451 PRO B 452 -1 O GLU B 451 N TRP B 202 LINK NA NA A 1 OD1 ASP A 274 1555 1555 2.66 LINK OE1 GLU A 426 MN MN A1001 1555 1555 2.49 LINK OE2 GLU A 426 MN MN A1001 1555 1555 2.41 LINK O3G ANP A1000 MN MN A1001 1555 1555 2.32 LINK O2B ANP A1000 MN MN A1001 1555 1555 2.23 LINK O1A ANP A1000 MN MN A1001 1555 1555 2.24 LINK O HOH B 174 MN MN B1001 1555 1555 2.44 LINK OE1 GLU B 426 MN MN B1001 1555 1555 2.44 LINK OE2 GLU B 426 MN MN B1001 1555 1555 2.42 LINK O1B ANP B1000 MN MN B1001 1555 1555 2.25 LINK O1A ANP B1000 MN MN B1001 1555 1555 2.45 CISPEP 1 TRP A 407 PRO A 408 0 10.06 CISPEP 2 LEU A 433 GLY A 434 0 -0.86 CISPEP 3 TRP B 407 PRO B 408 0 2.88 CISPEP 4 LEU B 433 GLY B 434 0 -10.70 SITE 1 AC1 14 HOH A 12 HOH A 42 LYS A 200 ARG A 264 SITE 2 AC1 14 ARG A 266 LYS A 281 LYS A 294 TYR A 359 SITE 3 AC1 14 ARG A 361 GLU A 426 SER A 457 LYS A 458 SITE 4 AC1 14 HOH A 537 MN A1001 SITE 1 AC2 3 GLU A 426 HOH A 494 ANP A1000 SITE 1 AC3 6 SER A 272 THR A 273 ASP A 274 THR A 275 SITE 2 AC3 6 HOH A 486 HOH A 536 SITE 1 AC4 6 HOH A 154 HOH A 158 LYS A 300 ARG A 302 SITE 2 AC4 6 HIS A 303 LYS A 320 SITE 1 AC5 4 LYS A 396 HOH A 512 HOH B 26 ASN B 246 SITE 1 AC6 3 ASP A 274 GLU A 301 ARG A 302 SITE 1 AC7 16 HOH B 1 HOH B 127 HOH B 137 LYS B 200 SITE 2 AC7 16 TYR B 241 ARG B 264 ARG B 266 LYS B 281 SITE 3 AC7 16 LYS B 294 TYR B 359 ARG B 361 GLU B 426 SITE 4 AC7 16 PHE B 456 SER B 457 LYS B 458 MN B1001 SITE 1 AC8 3 HOH B 174 GLU B 426 ANP B1000 SITE 1 AC9 5 LYS A 470 HOH A 493 ARG B 302 HIS B 303 SITE 2 AC9 5 LYS B 320 SITE 1 BC1 8 HOH B 39 HOH B 104 ARG B 253 LYS B 256 SITE 2 BC1 8 HIS B 283 SER B 292 HOH B 491 HOH B 533 SITE 1 BC2 4 THR B 273 ASP B 274 THR B 275 HOH B 496 CRYST1 68.260 100.970 102.370 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 0.014650 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009768 0.00000