HEADER RNA BINDING PROTEIN 29-SEP-20 7K9B TITLE CRYSTAL STRUCTURE OF BACILLUS HALODURANS OAPB (NATIVE) AT 1.2 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: OLE-ASSOCIATED PROTEIN B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: OAPB; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS (STRAIN ATCC BAA-125 / DSM SOURCE 3 18197 / FERM 7344 / JCM 9153 / C-125); SOURCE 4 ORGANISM_TAXID: 272558; SOURCE 5 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 6 GENE: BH0157; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBONUCLEOPROTEIN COMPLEX, OLE RNA, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.YANG,R.R.BREAKER REVDAT 3 06-MAR-24 7K9B 1 REMARK REVDAT 2 10-MAR-21 7K9B 1 JRNL REVDAT 1 03-MAR-21 7K9B 0 JRNL AUTH Y.YANG,K.A.HARRIS,D.L.WIDNER,R.R.BREAKER JRNL TITL STRUCTURE OF A BACTERIAL OAPB PROTEIN WITH ITS OLE RNA JRNL TITL 2 TARGET GIVES INSIGHTS INTO THE ARCHITECTURE OF THE OLE JRNL TITL 3 RIBONUCLEOPROTEIN COMPLEX. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33619097 JRNL DOI 10.1073/PNAS.2020393118 REMARK 2 REMARK 2 RESOLUTION. 1.20 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 50644 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2530 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 47.9180 - 3.1510 0.98 2767 146 0.1496 0.1808 REMARK 3 2 3.1510 - 2.5010 0.99 2741 144 0.1364 0.1659 REMARK 3 3 2.5010 - 2.1849 1.00 2716 143 0.1168 0.1254 REMARK 3 4 2.1849 - 1.9851 0.99 2720 143 0.1063 0.1310 REMARK 3 5 1.9851 - 1.8428 0.97 2632 139 0.1063 0.1348 REMARK 3 6 1.8428 - 1.7342 1.00 2730 144 0.1064 0.1432 REMARK 3 7 1.7342 - 1.6473 1.00 2678 140 0.1043 0.1422 REMARK 3 8 1.6473 - 1.5756 0.99 2718 143 0.0959 0.1422 REMARK 3 9 1.5756 - 1.5149 1.00 2691 141 0.0936 0.1200 REMARK 3 10 1.5149 - 1.4627 1.00 2704 143 0.1000 0.1531 REMARK 3 11 1.4627 - 1.4169 0.95 2572 134 0.1040 0.1363 REMARK 3 12 1.4169 - 1.3764 0.99 2681 140 0.1058 0.1521 REMARK 3 13 1.3764 - 1.3402 0.99 2668 140 0.1080 0.1402 REMARK 3 14 1.3402 - 1.3075 0.99 2686 142 0.1097 0.1406 REMARK 3 15 1.3075 - 1.2778 0.99 2688 141 0.1152 0.1680 REMARK 3 16 1.2778 - 1.2506 0.99 2679 142 0.1275 0.1785 REMARK 3 17 1.2506 - 1.2255 0.99 2676 140 0.1261 0.1752 REMARK 3 18 1.2255 - 1.2024 0.88 2367 125 0.1300 0.1757 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.09 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 7K9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000252112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50673 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 47.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.15600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS-HCL (PH 8.5), 100 MM KCL, REMARK 280 10 MM MGCL2 AND 30% POLYETHYLENE GLYCOL (PEG) 400, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 17.45450 REMARK 290 SMTRY3 2 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 B 5 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 ASP A 21 38.25 -99.33 REMARK 500 ASP A 23 -1.19 77.94 REMARK 500 ASP A 43 -84.98 -137.60 REMARK 500 ASP A 43 -81.92 -137.60 REMARK 500 ASP B 21 43.29 -103.30 REMARK 500 ASP B 43 -82.27 -138.28 REMARK 500 ASP B 43 -74.49 -144.93 REMARK 500 REMARK 500 REMARK: NULL 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 431 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH B 475 DISTANCE = 6.11 ANGSTROMS REMARK 525 HOH B 476 DISTANCE = 6.69 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 201 DBREF 7K9B A 5 102 UNP Q9KGD7 Q9KGD7_BACHD 5 102 DBREF 7K9B B 5 102 UNP Q9KGD7 Q9KGD7_BACHD 5 102 SEQRES 1 A 98 GLY PRO SER PRO GLU ILE GLY GLN ILE VAL LYS ILE VAL SEQRES 2 A 98 LYS GLY ARG ASP ARG ASP GLN PHE SER VAL ILE ILE LYS SEQRES 3 A 98 ARG VAL ASP ASP ARG PHE VAL TYR ILE ALA ASP GLY ASP SEQRES 4 A 98 LYS ARG LYS VAL ASP ARG ALA LYS ARG LYS ASN MET ASN SEQRES 5 A 98 HIS LEU LYS LEU ILE ASP HIS ILE SER PRO GLU VAL ARG SEQRES 6 A 98 HIS SER PHE GLU GLU THR GLY LYS VAL THR ASN GLY LYS SEQRES 7 A 98 LEU ARG PHE ALA LEU LYS LYS PHE LEU GLU GLU HIS ALA SEQRES 8 A 98 ASP LEU LEU LYS GLU GLY GLU SEQRES 1 B 98 GLY PRO SER PRO GLU ILE GLY GLN ILE VAL LYS ILE VAL SEQRES 2 B 98 LYS GLY ARG ASP ARG ASP GLN PHE SER VAL ILE ILE LYS SEQRES 3 B 98 ARG VAL ASP ASP ARG PHE VAL TYR ILE ALA ASP GLY ASP SEQRES 4 B 98 LYS ARG LYS VAL ASP ARG ALA LYS ARG LYS ASN MET ASN SEQRES 5 B 98 HIS LEU LYS LEU ILE ASP HIS ILE SER PRO GLU VAL ARG SEQRES 6 B 98 HIS SER PHE GLU GLU THR GLY LYS VAL THR ASN GLY LYS SEQRES 7 B 98 LEU ARG PHE ALA LEU LYS LYS PHE LEU GLU GLU HIS ALA SEQRES 8 B 98 ASP LEU LEU LYS GLU GLY GLU HET CL A 201 1 HET CL B 201 1 HETNAM CL CHLORIDE ION FORMUL 3 CL 2(CL 1-) FORMUL 5 HOH *307(H2 O) HELIX 1 AA1 LYS A 46 ALA A 50 5 5 HELIX 2 AA2 SER A 65 GLY A 76 1 12 HELIX 3 AA3 THR A 79 HIS A 94 1 16 HELIX 4 AA4 HIS A 94 LYS A 99 1 6 HELIX 5 AA5 LYS B 46 ALA B 50 5 5 HELIX 6 AA6 SER B 65 GLY B 76 1 12 HELIX 7 AA7 THR B 79 HIS B 94 1 16 HELIX 8 AA8 ALA B 95 LYS B 99 5 5 SHEET 1 AA1 5 LYS A 51 ASN A 54 0 SHEET 2 AA1 5 PHE A 36 ALA A 40 -1 N VAL A 37 O LYS A 53 SHEET 3 AA1 5 PHE A 25 ARG A 31 -1 N ILE A 29 O TYR A 38 SHEET 4 AA1 5 GLN A 12 ILE A 16 -1 N GLN A 12 O ILE A 28 SHEET 5 AA1 5 LEU A 58 ILE A 64 -1 O LYS A 59 N LYS A 15 SHEET 1 AA2 5 LYS B 51 ASN B 54 0 SHEET 2 AA2 5 PHE B 36 ALA B 40 -1 N VAL B 37 O LYS B 53 SHEET 3 AA2 5 PHE B 25 ARG B 31 -1 N ILE B 29 O TYR B 38 SHEET 4 AA2 5 GLN B 12 ILE B 16 -1 N VAL B 14 O SER B 26 SHEET 5 AA2 5 LEU B 58 ILE B 64 -1 O HIS B 63 N ILE B 13 SITE 1 AC1 5 ARG A 20 ASP A 21 ARG A 45 LYS A 53 SITE 2 AC1 5 HOH A 305 SITE 1 AC2 4 ARG B 20 ASP B 21 ARG B 45 LYS B 53 CRYST1 47.918 34.909 49.811 90.00 90.24 90.00 P 1 21 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 0.020869 0.000000 0.000087 0.00000 SCALE2 0.000000 0.028646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020076 0.00000