HEADER BIOSYNTHETIC PROTEIN 02-FEB-09 3G3U TITLE CRYSTAL STRUCTURE OF A EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX TITLE 2 WITH PYROPHOSPHATE 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 3G3U 1 REMARK SEQADV REVDAT 1 05-MAY-09 3G3U 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. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 41135 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2094 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 19.7686 - 6.3711 1.00 2600 162 0.1827 0.2222 REMARK 3 2 6.3711 - 5.0853 1.00 2587 179 0.1980 0.2250 REMARK 3 3 5.0853 - 4.4508 1.00 2683 111 0.1464 0.1884 REMARK 3 4 4.4508 - 4.0477 1.00 2602 121 0.1636 0.1979 REMARK 3 5 4.0477 - 3.7597 1.00 2662 128 0.1656 0.1880 REMARK 3 6 3.7597 - 3.5394 1.00 2621 138 0.1642 0.1743 REMARK 3 7 3.5394 - 3.3630 1.00 2618 151 0.1666 0.1863 REMARK 3 8 3.3630 - 3.2173 1.00 2621 134 0.1928 0.2324 REMARK 3 9 3.2173 - 3.0939 1.00 2644 122 0.2041 0.2849 REMARK 3 10 3.0939 - 2.9875 1.00 2634 147 0.1982 0.2498 REMARK 3 11 2.9875 - 2.8944 1.00 2595 167 0.2138 0.2403 REMARK 3 12 2.8944 - 2.8119 1.00 2618 141 0.2101 0.2759 REMARK 3 13 2.8119 - 2.7381 1.00 2608 148 0.2144 0.2613 REMARK 3 14 2.7381 - 2.6714 1.00 2655 129 0.2165 0.2882 REMARK 3 15 2.6714 - 2.6108 1.00 2610 129 0.2160 0.2832 REMARK 3 16 2.6108 - 2.5554 1.00 2647 166 0.2027 0.2550 REMARK 3 17 2.5554 - 2.5044 1.00 2607 131 0.2056 0.2728 REMARK 3 18 2.5044 - 2.4572 1.00 2629 118 0.2095 0.2485 REMARK 3 19 2.4572 - 2.4134 1.00 2633 162 0.2192 0.2722 REMARK 3 20 2.4134 - 2.3726 1.00 2631 131 0.2198 0.2970 REMARK 3 21 2.3726 - 2.3343 1.00 2613 138 0.2165 0.2798 REMARK 3 22 2.3343 - 2.2985 1.00 2617 154 0.2266 0.3382 REMARK 3 23 2.2985 - 2.2647 1.00 2623 139 0.2298 0.2700 REMARK 3 24 2.2647 - 2.2329 1.00 2672 121 0.2369 0.3392 REMARK 3 25 2.2329 - 2.2027 1.00 2557 153 0.2442 0.3102 REMARK 3 26 2.2027 - 2.1742 1.00 2661 134 0.2340 0.3081 REMARK 3 27 2.1742 - 2.1470 1.00 2575 154 0.2473 0.2573 REMARK 3 28 2.1470 - 2.1212 0.99 2652 126 0.2573 0.2837 REMARK 3 29 2.1212 - 2.0965 0.98 2528 144 0.2840 0.3087 REMARK 3 30 2.0965 - 2.0700 0.79 2079 110 0.3079 0.3690 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 : 0.34 REMARK 3 B_SOL : 50.37 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.40 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 : 0.007 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 3G3U 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_1000051388. 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 : 43477 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.62200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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 3G3R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.57 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 34.22000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.24500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.24500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.22000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.36500 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 GLN A 365 130.47 -171.28 REMARK 500 HIS B 218 -34.15 -141.01 REMARK 500 LYS B 326 -81.66 -62.39 REMARK 500 VAL B 354 -50.72 -129.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2 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 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 9 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: 3G3R RELATED DB: PDB REMARK 900 EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH APPNHP-MN2+ REMARK 900 RELATED ID: 3G3T RELATED DB: PDB REMARK 900 EUKARYOTIC POLYPHOSPHATE POLYMERASE IN COMPLEX WITH ORTHOPHOSPHATE 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 DBREF 3G3U A 189 480 UNP P47075 VTC4_YEAST 189 480 DBREF 3G3U B 189 480 UNP P47075 VTC4_YEAST 189 480 SEQADV 3G3U GLY A 186 UNP P47075 EXPRESSION TAG SEQADV 3G3U ALA A 187 UNP P47075 EXPRESSION TAG SEQADV 3G3U MET A 188 UNP P47075 EXPRESSION TAG SEQADV 3G3U GLY B 186 UNP P47075 EXPRESSION TAG SEQADV 3G3U ALA B 187 UNP P47075 EXPRESSION TAG SEQADV 3G3U 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 POP A1000 9 HET POP A1001 9 HET SO4 A 1 5 HET SO4 A 4 5 HET SO4 A 6 5 HET SO4 A 7 5 HET POP B1000 9 HET SO4 B 2 5 HET SO4 B 3 5 HET SO4 B 5 5 HET SO4 B 8 5 HET EDO B 9 4 HETNAM POP PYROPHOSPHATE 2- HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 POP 3(H2 O7 P2 2-) FORMUL 5 SO4 8(O4 S 2-) FORMUL 14 EDO C2 H6 O2 FORMUL 15 HOH *380(H2 O) HELIX 1 1 HIS A 204 ASP A 206 5 3 HELIX 2 2 ASN A 207 LYS A 217 1 11 HELIX 3 3 GLU A 231 ASP A 234 5 4 HELIX 4 4 LEU A 247 ARG A 255 1 9 HELIX 5 5 HIS A 303 LYS A 309 1 7 HELIX 6 6 THR A 313 GLY A 325 1 13 HELIX 7 7 PRO A 328 LYS A 349 1 22 HELIX 8 8 ASP A 413 LYS A 415 5 3 HELIX 9 9 PRO A 438 GLY A 446 1 9 HELIX 10 10 SER A 457 LEU A 467 1 11 HELIX 11 11 HIS B 204 ASP B 206 5 3 HELIX 12 12 ASN B 207 LEU B 216 1 10 HELIX 13 13 GLU B 231 ASP B 234 5 4 HELIX 14 14 LEU B 247 LYS B 256 1 10 HELIX 15 15 GLU B 285 GLY B 289 5 5 HELIX 16 16 HIS B 303 LYS B 309 1 7 HELIX 17 17 THR B 313 PHE B 318 1 6 HELIX 18 18 PHE B 318 GLU B 324 1 7 HELIX 19 19 PRO B 328 LYS B 349 1 22 HELIX 20 20 ASP B 413 LYS B 415 5 3 HELIX 21 21 PRO B 438 GLY B 446 1 9 HELIX 22 22 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 ARG A 280 O ALA A 295 SHEET 3 A 7 GLU A 261 TYR A 268 -1 N ARG A 266 O PHE A 277 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 ILE A 374 N PHE A 364 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 ARG A 280 O ALA A 295 SHEET 3 B 9 GLU A 261 TYR A 268 -1 N ARG A 266 O PHE A 277 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 ILE A 374 N PHE A 364 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 PHE B 242 O HIS B 263 SHEET 5 D 7 ARG B 352 GLN B 365 -1 O ARG B 352 N ASP B 243 SHEET 6 D 7 VAL B 372 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 PHE B 242 O HIS B 263 SHEET 5 E 9 ARG B 352 GLN B 365 -1 O ARG B 352 N ASP B 243 SHEET 6 E 9 VAL B 372 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 CISPEP 1 TRP A 407 PRO A 408 0 9.96 CISPEP 2 LEU A 433 GLY A 434 0 -1.05 CISPEP 3 TRP B 407 PRO B 408 0 6.26 CISPEP 4 LEU B 433 GLY B 434 0 -12.99 SITE 1 AC1 12 HOH A 10 TYR A 241 ARG A 264 ARG A 266 SITE 2 AC1 12 LYS A 281 LYS A 294 TYR A 359 ARG A 361 SITE 3 AC1 12 GLU A 426 LYS A 458 HOH A 558 POP A1001 SITE 1 AC2 12 HOH A 13 HOH A 39 LYS A 200 TYR A 241 SITE 2 AC2 12 ARG A 264 LYS A 281 PHE A 456 SER A 457 SITE 3 AC2 12 LYS A 458 PHE A 459 HOH A 507 POP A1000 SITE 1 AC3 4 THR A 273 ASP A 274 THR A 275 HOH A 506 SITE 1 AC4 6 HOH A 139 LYS A 300 ARG A 302 HIS A 303 SITE 2 AC4 6 LYS A 320 HOH A 537 SITE 1 AC5 5 LYS A 396 HOH A 490 HOH A 539 HOH B 23 SITE 2 AC5 5 ASN B 246 SITE 1 AC6 8 HOH A 41 HOH A 105 ARG A 253 LYS A 256 SITE 2 AC6 8 HIS A 283 LYS A 291 SER A 292 HOH A 528 SITE 1 AC7 11 HOH B 1 TYR B 241 ARG B 264 ARG B 266 SITE 2 AC7 11 LYS B 294 TYR B 359 ARG B 361 GLU B 426 SITE 3 AC7 11 LYS B 458 HOH B 530 HOH B 585 SITE 1 AC8 6 HOH A 181 LYS A 470 ARG B 302 HIS B 303 SITE 2 AC8 6 LYS B 320 HOH B 549 SITE 1 AC9 7 HOH B 36 HOH B 94 LYS B 256 HIS B 283 SITE 2 AC9 7 SER B 292 LYS B 455 HOH B 503 SITE 1 BC1 3 THR B 273 ASP B 274 THR B 275 SITE 1 BC2 6 HOH A 157 HOH B 52 ILE B 208 THR B 378 SITE 2 BC2 6 GLU B 379 PRO B 421 SITE 1 BC3 4 TYR B 241 ARG B 253 LYS B 281 SER B 457 CRYST1 68.440 100.730 102.490 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 0.014611 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009757 0.00000