HEADER HYDROLASE 15-NOV-19 6TG6 TITLE TOPRIM DOMAIN OF RNASE M5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE M5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE M5,RIBOSOMAL RNA TERMINAL MATURASE M5; COMPND 5 EC: 3.1.26.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: RNMV_1, RNMV, AVP43_02013; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNASE M5, RNASE, RRNA, 5S RRNA, PRECURSOR RRNA, PRE-5S RRNA, KEYWDS 2 RIBOSOMAL RNA, RIBONUCLEASE, CATALYTIC DOMAIN, TOPRIM DOMAIN, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.OERUM,M.CATALA,C.TISNE REVDAT 4 01-MAY-24 6TG6 1 REMARK REVDAT 3 28-OCT-20 6TG6 1 JRNL REVDAT 2 14-OCT-20 6TG6 1 JRNL REVDAT 1 23-SEP-20 6TG6 0 JRNL AUTH S.OERUM,T.DENDOOVEN,M.CATALA,L.GILET,C.DEGUT,A.TRINQUIER, JRNL AUTH 2 M.BOURGUET,P.BARRAUD,S.CIANFERANI,B.F.LUISI,C.CONDON,C.TISNE JRNL TITL STRUCTURES OF B. SUBTILIS MATURATION RNASES CAPTURED ON 50S JRNL TITL 2 RIBOSOME WITH PRE-RRNAS. JRNL REF MOL.CELL V. 80 227 2020 JRNL REFN ISSN 1097-2765 JRNL PMID 32991829 JRNL DOI 10.1016/J.MOLCEL.2020.09.008 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 23306 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1163 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 40.5500 - 2.5946 0.97 2916 151 0.2063 0.2053 REMARK 3 2 2.5946 - 2.0594 0.99 2817 149 0.1921 0.1990 REMARK 3 3 2.0594 - 1.7991 1.00 2772 146 0.1634 0.1852 REMARK 3 4 1.7991 - 1.6346 1.00 2782 145 0.1742 0.1823 REMARK 3 5 1.6346 - 1.5174 1.00 2753 145 0.1692 0.2042 REMARK 3 6 1.5174 - 1.4279 1.00 2763 146 0.1784 0.1921 REMARK 3 7 1.4279 - 1.3564 1.00 2742 144 0.2020 0.2257 REMARK 3 8 1.3564 - 1.3000 0.95 2598 137 0.2381 0.2622 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.62 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 : NULL NULL REMARK 3 ANGLE : NULL 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 6TG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23385 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.297 REMARK 200 RESOLUTION RANGE LOW (A) : 40.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.04920 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.2800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.760 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: HOMOLOGY MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 1.4 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 18.98500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.98500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.55000 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 DBREF1 6TG6 A 1 113 UNP A0A161UFV3_GEOSE DBREF2 6TG6 A A0A161UFV3 34 146 SEQADV 6TG6 GLY A -2 UNP A0A161UFV EXPRESSION TAG SEQADV 6TG6 GLY A -1 UNP A0A161UFV EXPRESSION TAG SEQADV 6TG6 SER A 0 UNP A0A161UFV EXPRESSION TAG SEQRES 1 A 116 GLY GLY SER MET LYS ILE LYS GLU VAL ILE VAL VAL GLU SEQRES 2 A 116 GLY LYS ASP ASP THR ALA ALA ILE ARG ARG ALA VAL ASP SEQRES 3 A 116 ALA ASP THR ILE GLU THR ASN GLY ALA ALA VAL GLY ALA SEQRES 4 A 116 GLU VAL ILE GLU ARG ILE LYS LEU ALA LYS GLU ARG ARG SEQRES 5 A 116 GLY VAL ILE ILE PHE THR ASP PRO ASP PHE PRO GLY GLU SEQRES 6 A 116 LYS ILE ARG ARG THR ILE ALA GLU GLN VAL PRO GLY CYS SEQRES 7 A 116 LYS HIS ALA PHE LEU PRO ARG GLU ALA ALA LYS ALA ARG SEQRES 8 A 116 SER GLY LYS GLY ILE GLY VAL GLU HIS ALA SER PRO ASP SEQRES 9 A 116 ASP ILE ARG GLN ALA LEU ALA ASN VAL TYR GLU GLU FORMUL 2 HOH *98(H2 O) HELIX 1 AA1 GLY A 11 ARG A 20 1 10 HELIX 2 AA2 GLY A 35 GLY A 50 1 16 HELIX 3 AA3 ASP A 58 VAL A 72 1 15 HELIX 4 AA4 PRO A 81 LYS A 86 1 6 HELIX 5 AA5 GLY A 94 ALA A 98 5 5 HELIX 6 AA6 SER A 99 ASN A 109 1 11 SHEET 1 AA1 4 THR A 26 GLU A 28 0 SHEET 2 AA1 4 VAL A 6 VAL A 9 1 N VAL A 9 O ILE A 27 SHEET 3 AA1 4 VAL A 51 ILE A 53 1 O ILE A 52 N VAL A 8 SHEET 4 AA1 4 LYS A 76 HIS A 77 1 O LYS A 76 N ILE A 53 CRYST1 37.970 81.100 29.910 90.00 90.00 90.00 P 21 21 2 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 0.026337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033434 0.00000