HEADER RNA BINDING PROTEIN 21-DEC-19 6VCR TITLE CRYSTAL STRUCTURE OF E.COLI RPPH IN COMPLEX WITH CTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA PYROPHOSPHOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: (DI)NUCLEOSIDE POLYPHOSPHATE HYDROLASE,AP5A PYROPHOSPHATASE; COMPND 5 EC: 3.6.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI S88; SOURCE 3 ORGANISM_TAXID: 585035; SOURCE 4 GENE: RPPH, NUDH, YGDP, B2830, JW2798; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RNA DEGRADATION, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GAO,N.VASILYEV,A.KAUSHIK,W.DUAN,A.SERGANOV REVDAT 3 11-OCT-23 6VCR 1 REMARK REVDAT 2 22-APR-20 6VCR 1 JRNL REVDAT 1 05-FEB-20 6VCR 0 JRNL AUTH A.GAO,N.VASILYEV,A.KAUSHIK,W.DUAN,A.SERGANOV JRNL TITL PRINCIPLES OF RNA AND NUCLEOTIDE DISCRIMINATION BY THE RNA JRNL TITL 2 PROCESSING ENZYME RPPH. JRNL REF NUCLEIC ACIDS RES. V. 48 3776 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 31960065 JRNL DOI 10.1093/NAR/GKAA024 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3546 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 22688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1135 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 19.3100 - 3.2000 1.00 2787 147 0.1608 0.1870 REMARK 3 2 3.2000 - 2.5400 1.00 2736 144 0.1651 0.1643 REMARK 3 3 2.5400 - 2.2200 1.00 2713 143 0.1586 0.1942 REMARK 3 4 2.2200 - 2.0200 1.00 2704 142 0.1536 0.1998 REMARK 3 5 2.0200 - 1.8700 1.00 2696 142 0.1645 0.2027 REMARK 3 6 1.8700 - 1.7600 1.00 2690 142 0.1743 0.2067 REMARK 3 7 1.7600 - 1.6700 0.99 2672 140 0.1897 0.2263 REMARK 3 8 1.6700 - 1.6000 0.94 2555 135 0.2021 0.2374 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.139 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.785 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.41 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 : 0.008 1436 REMARK 3 ANGLE : 1.340 1967 REMARK 3 CHIRALITY : 0.053 198 REMARK 3 PLANARITY : 0.006 235 REMARK 3 DIHEDRAL : 18.994 533 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 6VCR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000245150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: PHENIX REMARK 200 STARTING MODEL: 4S2Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M (NH4)2SO4, 10% (V/V) PEG3350, REMARK 280 10% (V/V) GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 39.26250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.40550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.26250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.40550 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASP A 4 CG OD1 OD2 REMARK 470 ARG A 72 CD NE CZ NH1 NH2 REMARK 470 LYS A 81 CD CE NZ REMARK 470 ARG A 82 CD NE CZ NH1 NH2 REMARK 470 ARG A 85 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 89 CB CG CD CE NZ REMARK 470 ARG A 134 CG CD NE CZ NH1 NH2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 486 DISTANCE = 6.19 ANGSTROMS 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 CTP A 202 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CTP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CTP A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CTP A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PPV A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VCN RELATED DB: PDB REMARK 900 6VCN CONTAINS THE SAME PROTEIN IN COMPLEX WITH PPCPG REMARK 900 RELATED ID: 6VCO RELATED DB: PDB REMARK 900 6VCO CONTAINS THE SAME PROTEIN IN COMPLEX WITH PPCPA REMARK 900 RELATED ID: 6VCP RELATED DB: PDB REMARK 900 6VCP CONTAINS THE SAME PROTEIN IN COMPLEX WITH UTP REMARK 900 RELATED ID: 6VCQ RELATED DB: PDB REMARK 900 6VCQ CONTAINS THE SAME PROTEIN IN COMPLEX WITH GTP REMARK 900 RELATED ID: 6VCK RELATED DB: PDB REMARK 900 6VCK CONTAINS THE SAME PROTEIN IN COMPLEX WITH DAPF AND GDP REMARK 900 RELATED ID: 6VCL RELATED DB: PDB REMARK 900 6VCL CONTAINS THE SAME PROTEIN IN COMPLEX WITH DAPF AND PPPGPP REMARK 900 RELATED ID: 6VCM RELATED DB: PDB REMARK 900 6VCM CONTAINS THE SAME PROTEIN IN COMPLEX WITH DAPF AND GTP DBREF 6VCR A 1 160 UNP P0A776 RPPH_ECOLI 1 160 SEQADV 6VCR SER A 0 UNP P0A776 EXPRESSION TAG SEQADV 6VCR ALA A 159 UNP P0A776 GLN 159 ENGINEERED MUTATION SEQADV 6VCR ALA A 160 UNP P0A776 GLU 160 ENGINEERED MUTATION SEQRES 1 A 161 SER MET ILE ASP ASP ASP GLY TYR ARG PRO ASN VAL GLY SEQRES 2 A 161 ILE VAL ILE CYS ASN ARG GLN GLY GLN VAL MET TRP ALA SEQRES 3 A 161 ARG ARG PHE GLY GLN HIS SER TRP GLN PHE PRO GLN GLY SEQRES 4 A 161 GLY ILE ASN PRO GLY GLU SER ALA GLU GLN ALA MET TYR SEQRES 5 A 161 ARG GLU LEU PHE GLU GLU VAL GLY LEU SER ARG LYS ASP SEQRES 6 A 161 VAL ARG ILE LEU ALA SER THR ARG ASN TRP LEU ARG TYR SEQRES 7 A 161 LYS LEU PRO LYS ARG LEU VAL ARG TRP ASP THR LYS PRO SEQRES 8 A 161 VAL CYS ILE GLY GLN LYS GLN LYS TRP PHE LEU LEU GLN SEQRES 9 A 161 LEU VAL SER GLY ASP ALA GLU ILE ASN MET GLN THR SER SEQRES 10 A 161 SER THR PRO GLU PHE ASP GLY TRP ARG TRP VAL SER TYR SEQRES 11 A 161 TRP TYR PRO VAL ARG GLN VAL VAL SER PHE LYS ARG ASP SEQRES 12 A 161 VAL TYR ARG ARG VAL MET LYS GLU PHE ALA SER VAL VAL SEQRES 13 A 161 MET SER LEU ALA ALA HET CTP A 201 40 HET CTP A 202 36 HET CTP A 203 41 HET PPV A 204 9 HET SO4 A 205 5 HETNAM CTP CYTIDINE-5'-TRIPHOSPHATE HETNAM PPV PYROPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 CTP 3(C9 H16 N3 O14 P3) FORMUL 5 PPV H4 O7 P2 FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *186(H2 O) HELIX 1 AA1 SER A 45 GLY A 59 1 15 HELIX 2 AA2 SER A 61 LYS A 63 5 3 HELIX 3 AA3 PRO A 80 VAL A 84 5 5 HELIX 4 AA4 GLY A 107 ILE A 111 5 5 HELIX 5 AA5 TRP A 130 VAL A 136 1 7 HELIX 6 AA6 VAL A 137 PHE A 139 5 3 HELIX 7 AA7 LYS A 140 ALA A 160 1 21 SHEET 1 AA1 4 GLN A 37 GLY A 39 0 SHEET 2 AA1 4 TYR A 7 CYS A 16 -1 N VAL A 11 O GLY A 38 SHEET 3 AA1 4 GLY A 94 LEU A 104 1 O LEU A 102 N VAL A 14 SHEET 4 AA1 4 VAL A 65 SER A 70 -1 N LEU A 68 O LEU A 101 SHEET 1 AA2 4 GLN A 37 GLY A 39 0 SHEET 2 AA2 4 TYR A 7 CYS A 16 -1 N VAL A 11 O GLY A 38 SHEET 3 AA2 4 GLY A 94 LEU A 104 1 O LEU A 102 N VAL A 14 SHEET 4 AA2 4 LEU A 75 LYS A 78 -1 N LEU A 75 O GLN A 97 SHEET 1 AA3 3 TRP A 33 GLN A 34 0 SHEET 2 AA3 3 VAL A 22 ARG A 27 -1 N ALA A 25 O GLN A 34 SHEET 3 AA3 3 PHE A 121 VAL A 127 -1 O ARG A 125 N TRP A 24 CISPEP 1 LYS A 89 PRO A 90 0 -11.49 SITE 1 AC1 17 ARG A 27 GLN A 30 SER A 32 GLN A 37 SITE 2 AC1 17 TYR A 77 LEU A 79 GLN A 95 LYS A 140 SITE 3 AC1 17 HOH A 307 HOH A 330 HOH A 337 HOH A 355 SITE 4 AC1 17 HOH A 362 HOH A 372 HOH A 402 HOH A 406 SITE 5 AC1 17 HOH A 433 SITE 1 AC2 8 TRP A 74 ARG A 76 ARG A 141 ASP A 142 SITE 2 AC2 8 ARG A 146 CTP A 203 HOH A 303 HOH A 373 SITE 1 AC3 8 TYR A 7 ARG A 76 LYS A 78 ARG A 141 SITE 2 AC3 8 ASP A 142 ARG A 146 CTP A 202 HOH A 312 SITE 1 AC4 6 SER A 45 ALA A 46 TYR A 131 GLN A 135 SITE 2 AC4 6 HOH A 306 HOH A 338 SITE 1 AC5 5 THR A 71 ARG A 72 ASN A 73 GLU A 150 SITE 2 AC5 5 HOH A 327 CRYST1 78.525 38.811 57.692 90.00 99.02 90.00 C 1 2 1 4 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 0.012735 0.000000 0.002022 0.00000 SCALE2 0.000000 0.025766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017551 0.00000