HEADER RNA BINDING PROTEIN 21-DEC-19 6VCP TITLE CRYSTAL STRUCTURE OF E.COLI RPPH IN COMPLEX WITH UTP 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 6VCP 1 REMARK REVDAT 2 22-APR-20 6VCP 1 JRNL REVDAT 1 05-FEB-20 6VCP 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. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 19236 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 961 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 19.3700 - 3.2500 0.99 2683 142 0.1639 0.1739 REMARK 3 2 3.2500 - 2.5800 1.00 2626 138 0.1853 0.2157 REMARK 3 3 2.5800 - 2.2500 1.00 2629 138 0.1836 0.2261 REMARK 3 4 2.2500 - 2.0500 1.00 2610 138 0.1774 0.2427 REMARK 3 5 2.0500 - 1.9000 1.00 2568 135 0.1890 0.2260 REMARK 3 6 1.9000 - 1.7900 1.00 2621 138 0.2116 0.2393 REMARK 3 7 1.7900 - 1.7000 0.97 2538 132 0.2585 0.2867 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) : 0.164 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.671 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.47 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 : 0.011 1381 REMARK 3 ANGLE : 1.209 1882 REMARK 3 CHIRALITY : 0.064 191 REMARK 3 PLANARITY : 0.007 229 REMARK 3 DIHEDRAL : 18.493 486 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 6VCP 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_1000245157. 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 : 19245 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 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 (%): 47.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 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 39.39150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.36950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.39150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.36950 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 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 ASP A 87 REMARK 465 THR A 88 REMARK 465 LYS A 89 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 ARG A 72 CG 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 ARG A 134 CD NE CZ NH1 NH2 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 ASN A 17 -165.34 -113.17 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 UTP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UTP A 202 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: 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 6VCP A 1 160 UNP P0A776 RPPH_ECOLI 1 160 SEQADV 6VCP SER A 0 UNP P0A776 EXPRESSION TAG SEQADV 6VCP ALA A 159 UNP P0A776 GLN 159 ENGINEERED MUTATION SEQADV 6VCP 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 UTP A 201 29 HET UTP A 202 29 HETNAM UTP URIDINE 5'-TRIPHOSPHATE FORMUL 2 UTP 2(C9 H15 N2 O15 P3) FORMUL 4 HOH *151(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 CYS A 16 SHEET 4 AA1 4 VAL A 65 SER A 70 -1 N ALA A 69 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 CYS A 16 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 GLN A 21 ARG A 27 -1 N ALA A 25 O GLN A 34 SHEET 3 AA3 3 PHE A 121 SER A 128 -1 O ARG A 125 N TRP A 24 SITE 1 AC1 17 ARG A 8 ARG A 27 SER A 32 GLN A 37 SITE 2 AC1 17 TYR A 77 LEU A 79 LEU A 83 GLN A 95 SITE 3 AC1 17 VAL A 137 PHE A 139 LYS A 140 HOH A 311 SITE 4 AC1 17 HOH A 335 HOH A 354 HOH A 368 HOH A 370 SITE 5 AC1 17 HOH A 384 SITE 1 AC2 17 HIS A 31 TRP A 33 GLY A 43 GLU A 44 SITE 2 AC2 17 SER A 45 ALA A 46 GLN A 48 THR A 115 SITE 3 AC2 17 ARG A 125 TYR A 131 GLN A 135 HOH A 318 SITE 4 AC2 17 HOH A 325 HOH A 333 HOH A 347 HOH A 351 SITE 5 AC2 17 HOH A 395 CRYST1 78.783 38.739 58.757 90.00 101.01 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 0.012693 0.000000 0.002469 0.00000 SCALE2 0.000000 0.025814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017338 0.00000