HEADER RNA BINDING PROTEIN 12-APR-18 6D1R TITLE STRUCTURE OF STAPHYLOCOCCUS AUREUS RNASE P PROTEIN AT 2.0 ANGSTROM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE P PROTEIN COMPONENT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASEP PROTEIN,PROTEIN C5; COMPND 5 EC: 3.1.26.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: RNPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RNASE, P PROTEIN, TRNA PROCESSING, RNA METABOLISM, RNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.HA,J.COLQUHOUN,N.NOINAJ,C.DAS,P.DUNMAN,D.P.FLAHERTY REVDAT 3 13-MAR-24 6D1R 1 REMARK REVDAT 2 17-OCT-18 6D1R 1 JRNL REVDAT 1 26-SEP-18 6D1R 0 JRNL AUTH L.HA,J.COLQUHOUN,N.NOINAJ,C.DAS,P.M.DUNMAN,D.P.FLAHERTY JRNL TITL CRYSTAL STRUCTURE OF THE RIBONUCLEASE-P-PROTEIN SUBUNIT FROM JRNL TITL 2 STAPHYLOCOCCUS AUREUS. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 74 632 2018 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 30279314 JRNL DOI 10.1107/S2053230X18011512 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 12309 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1223 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 31.2496 - 4.1477 1.00 1323 149 0.1995 0.2265 REMARK 3 2 4.1477 - 3.2933 1.00 1251 133 0.1948 0.2035 REMARK 3 3 3.2933 - 2.8773 1.00 1255 135 0.2214 0.2312 REMARK 3 4 2.8773 - 2.6144 1.00 1247 135 0.2220 0.2652 REMARK 3 5 2.6144 - 2.4271 1.00 1231 137 0.2197 0.2368 REMARK 3 6 2.4271 - 2.2840 1.00 1211 135 0.2258 0.2333 REMARK 3 7 2.2840 - 2.1697 1.00 1218 140 0.2399 0.2652 REMARK 3 8 2.1697 - 2.0753 1.00 1225 136 0.2670 0.3150 REMARK 3 9 2.0753 - 1.9954 0.91 1125 123 0.3237 0.3430 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.79 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 : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3618 18.9090 14.9603 REMARK 3 T TENSOR REMARK 3 T11: 0.5822 T22: 0.4445 REMARK 3 T33: 0.3758 T12: 0.2045 REMARK 3 T13: -0.0507 T23: -0.0296 REMARK 3 L TENSOR REMARK 3 L11: 4.2640 L22: 5.8124 REMARK 3 L33: 4.8929 L12: 0.0437 REMARK 3 L13: 0.8945 L23: -0.3540 REMARK 3 S TENSOR REMARK 3 S11: 0.1570 S12: 0.4580 S13: -0.6207 REMARK 3 S21: -0.6166 S22: -0.1432 S23: -0.2305 REMARK 3 S31: 1.4523 S32: 0.5687 S33: 0.0935 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.1304 30.0675 15.1084 REMARK 3 T TENSOR REMARK 3 T11: 0.3362 T22: 0.2537 REMARK 3 T33: 0.3137 T12: 0.0278 REMARK 3 T13: -0.0572 T23: 0.0040 REMARK 3 L TENSOR REMARK 3 L11: 3.5267 L22: 3.1290 REMARK 3 L33: 4.3987 L12: -0.5377 REMARK 3 L13: -3.5135 L23: 0.5990 REMARK 3 S TENSOR REMARK 3 S11: 0.0366 S12: 0.2846 S13: -0.2383 REMARK 3 S21: -0.2744 S22: -0.0678 S23: 0.3665 REMARK 3 S31: 0.2265 S32: -0.1772 S33: 0.0069 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 73 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.8769 30.2049 19.9359 REMARK 3 T TENSOR REMARK 3 T11: 0.2912 T22: 0.4397 REMARK 3 T33: 0.2817 T12: 0.0333 REMARK 3 T13: -0.0390 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 4.0267 L22: 5.6816 REMARK 3 L33: 6.2709 L12: -0.2734 REMARK 3 L13: -1.5693 L23: 0.0103 REMARK 3 S TENSOR REMARK 3 S11: 0.0443 S12: -0.0647 S13: 0.1320 REMARK 3 S21: -0.0732 S22: -0.0162 S23: -0.4153 REMARK 3 S31: -0.0246 S32: 0.7068 S33: -0.0482 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 6D1R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233180. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12313 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 1.21600 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: PHASER 2.7.16 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.3M (NH4)2SO4, 0.15M POTASSIUM REMARK 280 PHOSPHATE PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 231 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 TRP A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 114 REMARK 465 LYS A 115 REMARK 465 ILE A 116 REMARK 465 LYS A 117 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 8 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 10 CG CD CE NZ REMARK 470 LYS A 11 CG CD CE NZ REMARK 470 LYS A 20 CG CD CE NZ REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 ASN A 113 CG OD1 ND2 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 27 -168.94 -102.56 REMARK 500 REMARK 500 REMARK: NULL DBREF 6D1R A 4 117 UNP P0A0H5 RNPA_STAAU 4 117 SEQADV 6D1R GLY A -1 UNP P0A0H5 EXPRESSION TAG SEQADV 6D1R ALA A 0 UNP P0A0H5 EXPRESSION TAG SEQADV 6D1R MET A 1 UNP P0A0H5 EXPRESSION TAG SEQADV 6D1R GLY A 2 UNP P0A0H5 EXPRESSION TAG SEQADV 6D1R TRP A 3 UNP P0A0H5 EXPRESSION TAG SEQRES 1 A 119 GLY ALA MET GLY TRP GLU LYS ALA TYR ARG ILE LYS LYS SEQRES 2 A 119 ASN ALA ASP PHE GLN ARG ILE TYR LYS LYS GLY HIS SER SEQRES 3 A 119 VAL ALA ASN ARG GLN PHE VAL VAL TYR THR CYS ASN ASN SEQRES 4 A 119 LYS GLU ILE ASP HIS PHE ARG LEU GLY ILE SER VAL SER SEQRES 5 A 119 LYS LYS LEU GLY ASN ALA VAL LEU ARG ASN LYS ILE LYS SEQRES 6 A 119 ARG ALA ILE ARG GLU ASN PHE LYS VAL HIS LYS SER HIS SEQRES 7 A 119 ILE LEU ALA LYS ASP ILE ILE VAL ILE ALA ARG GLN PRO SEQRES 8 A 119 ALA LYS ASP MET THR THR LEU GLN ILE GLN ASN SER LEU SEQRES 9 A 119 GLU HIS VAL LEU LYS ILE ALA LYS VAL PHE ASN LYS LYS SEQRES 10 A 119 ILE LYS FORMUL 2 HOH *36(H2 O) HELIX 1 AA1 LYS A 11 GLY A 22 1 12 HELIX 2 AA2 ASN A 55 HIS A 73 1 19 HELIX 3 AA3 LYS A 74 ILE A 77 5 4 HELIX 4 AA4 GLN A 88 MET A 93 5 6 HELIX 5 AA5 THR A 94 ALA A 109 1 16 SHEET 1 AA1 4 HIS A 23 ALA A 26 0 SHEET 2 AA1 4 PHE A 30 ASN A 36 -1 O VAL A 32 N VAL A 25 SHEET 3 AA1 4 LYS A 80 ALA A 86 -1 O ILE A 85 N VAL A 31 SHEET 4 AA1 4 ARG A 44 SER A 48 1 N GLY A 46 O VAL A 84 CRYST1 72.159 72.159 58.958 90.00 90.00 120.00 P 3 2 1 6 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 0.013858 0.008001 0.000000 0.00000 SCALE2 0.000000 0.016002 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016961 0.00000