HEADER RNA BINDING PROTEIN 15-NOV-19 6TGJ TITLE RNA-BINDING DOMAIN OF RNASE M5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE M5; COMPND 3 CHAIN: A, B; 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, NOVEL FOLD, RNA-BINDING DOMAIN, RNA KEYWDS 3 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.OERUM,M.CATALA,C.DEGUT,C.TISNE REVDAT 4 15-MAY-24 6TGJ 1 REMARK REVDAT 3 28-OCT-20 6TGJ 1 JRNL REVDAT 2 14-OCT-20 6TGJ 1 JRNL REVDAT 1 30-SEP-20 6TGJ 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 24138 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1210 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 36.4920 - 3.1124 1.00 2746 159 0.1822 0.2257 REMARK 3 2 3.1124 - 2.4705 1.00 2630 137 0.2156 0.2668 REMARK 3 3 2.4705 - 2.1583 0.99 2571 145 0.2132 0.2500 REMARK 3 4 2.1583 - 1.9610 0.98 2559 119 0.2214 0.2736 REMARK 3 5 1.9610 - 1.8204 0.98 2505 154 0.2441 0.2625 REMARK 3 6 1.8204 - 1.7131 0.98 2543 123 0.2404 0.3445 REMARK 3 7 1.7131 - 1.6273 0.99 2491 141 0.2627 0.2739 REMARK 3 8 1.6273 - 1.5565 0.98 2517 109 0.2792 0.2840 REMARK 3 9 1.5565 - 1.5000 0.92 2366 123 0.3183 0.3693 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.19 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 6TGJ 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_1292105428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-14 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 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24152 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.497 REMARK 200 RESOLUTION RANGE LOW (A) : 36.492 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04584 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.43100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.140 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CACODYLATE PH 6.5, 0.2 AMMONIUM REMARK 280 SULFATE AND 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 13.90050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.49250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.29700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.49250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.90050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.29700 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 98 REMARK 465 GLY A 99 REMARK 465 SER A 100 REMARK 465 MET A 101 REMARK 465 LYS A 102 REMARK 465 ILE A 103 REMARK 465 LYS A 104 REMARK 465 GLN A 105 REMARK 465 ALA A 106 REMARK 465 LEU A 107 REMARK 465 ALA A 108 REMARK 465 ASN A 109 REMARK 465 VAL A 110 REMARK 465 TYR A 111 REMARK 465 GLU A 112 REMARK 465 GLU A 113 REMARK 465 THR A 114 REMARK 465 ALA A 115 REMARK 465 ASP A 116 REMARK 465 GLY A 185 REMARK 465 ASP A 186 REMARK 465 ALA A 187 REMARK 465 GLY B 98 REMARK 465 GLY B 99 REMARK 465 SER B 100 REMARK 465 MET B 101 REMARK 465 LYS B 102 REMARK 465 ILE B 103 REMARK 465 LYS B 104 REMARK 465 GLN B 105 REMARK 465 ALA B 106 REMARK 465 LEU B 107 REMARK 465 ALA B 108 REMARK 465 ASN B 109 REMARK 465 VAL B 110 REMARK 465 TYR B 111 REMARK 465 GLU B 112 REMARK 465 GLU B 113 REMARK 465 THR B 114 REMARK 465 ALA B 115 REMARK 465 ASP B 116 REMARK 465 TRP B 117 REMARK 465 GLU B 118 REMARK 465 ALA B 187 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 GLU B 119 CG CD OE1 OE2 REMARK 470 ASP B 186 CG OD1 OD2 DBREF1 6TGJ A 105 187 UNP A0A161UFV3_GEOSE DBREF2 6TGJ A A0A161UFV3 138 220 DBREF1 6TGJ B 105 187 UNP A0A161UFV3_GEOSE DBREF2 6TGJ B A0A161UFV3 138 220 SEQADV 6TGJ GLY A 98 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ GLY A 99 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ SER A 100 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ MET A 101 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ LYS A 102 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ ILE A 103 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ LYS A 104 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ GLY B 98 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ GLY B 99 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ SER B 100 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ MET B 101 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ LYS B 102 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ ILE B 103 UNP A0A161UFV EXPRESSION TAG SEQADV 6TGJ LYS B 104 UNP A0A161UFV EXPRESSION TAG SEQRES 1 A 90 GLY GLY SER MET LYS ILE LYS GLN ALA LEU ALA ASN VAL SEQRES 2 A 90 TYR GLU GLU THR ALA ASP TRP GLU GLU GLU ILE THR PHE SEQRES 3 A 90 ALA GLU LEU ILE GLU ALA GLY LEU VAL GLY GLY GLU MET SEQRES 4 A 90 ALA ARG ARG ARG ARG GLN ARG LEU GLY GLU GLU LEU LYS SEQRES 5 A 90 ILE GLY TYR ALA ASN GLY ARG GLN PHE HIS LYS ARG LEU SEQRES 6 A 90 LYS VAL PHE ARG ILE SER ARG ASP ALA PHE TYR ALA ALA SEQRES 7 A 90 LEU ALA GLN VAL MET ARG GLU GLU ALA GLY ASP ALA SEQRES 1 B 90 GLY GLY SER MET LYS ILE LYS GLN ALA LEU ALA ASN VAL SEQRES 2 B 90 TYR GLU GLU THR ALA ASP TRP GLU GLU GLU ILE THR PHE SEQRES 3 B 90 ALA GLU LEU ILE GLU ALA GLY LEU VAL GLY GLY GLU MET SEQRES 4 B 90 ALA ARG ARG ARG ARG GLN ARG LEU GLY GLU GLU LEU LYS SEQRES 5 B 90 ILE GLY TYR ALA ASN GLY ARG GLN PHE HIS LYS ARG LEU SEQRES 6 B 90 LYS VAL PHE ARG ILE SER ARG ASP ALA PHE TYR ALA ALA SEQRES 7 B 90 LEU ALA GLN VAL MET ARG GLU GLU ALA GLY ASP ALA FORMUL 3 HOH *120(H2 O) HELIX 1 AA1 THR A 122 ALA A 129 1 8 HELIX 2 AA2 GLY A 134 LEU A 148 1 15 HELIX 3 AA3 ASN A 154 PHE A 165 1 12 HELIX 4 AA4 SER A 168 ALA A 184 1 17 HELIX 5 AA5 THR B 122 ALA B 129 1 8 HELIX 6 AA6 GLY B 134 LEU B 148 1 15 HELIX 7 AA7 GLN B 157 PHE B 165 1 9 HELIX 8 AA8 SER B 168 GLY B 185 1 18 CRYST1 27.801 72.594 72.985 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 0.035970 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013701 0.00000