HEADER HYDROLASE 22-JUN-22 7Y7O TITLE CRYSTAL STRUCTURE OF METALLO-ENDORIBONUCLEASE YBEY FROM STAPHYLOCOCCUS TITLE 2 AUREUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDORIBONUCLEASE YBEY; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50; SOURCE 3 ORGANISM_TAXID: 158878; SOURCE 4 STRAIN: MU50 / ATCC 700699; SOURCE 5 GENE: YBEY, SAV1570; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RNA, ENDORIBONUCLEASE, METALLOPROTEIN, ZINC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LEE,N.-C.HA REVDAT 1 08-MAR-23 7Y7O 0 JRNL AUTH J.LEE,I.JO,A.R.KWON,N.C.HA JRNL TITL CRYSTAL STRUCTURE OF THE METALLO-ENDORIBONUCLEASE YBEY FROM JRNL TITL 2 STAPHYLOCOCCUS AUREUS. JRNL REF J MICROBIOL BIOTECHNOL. V. 33 28 2023 JRNL REFN ESSN 1738-8872 JRNL PMID 36457189 JRNL DOI 10.4014/JMB.2209.09019 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 22298 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2002 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 43.5900 - 4.5800 0.99 1534 159 0.1779 0.2025 REMARK 3 2 4.5700 - 3.6300 0.99 1508 149 0.1598 0.1862 REMARK 3 3 3.6300 - 3.1700 0.99 1505 145 0.1965 0.2233 REMARK 3 4 3.1700 - 2.8800 0.98 1450 142 0.2257 0.2506 REMARK 3 5 2.8800 - 2.6800 0.98 1480 151 0.2267 0.2430 REMARK 3 6 2.6800 - 2.5200 0.98 1469 144 0.2056 0.2180 REMARK 3 7 2.5200 - 2.3900 0.97 1445 143 0.2087 0.2638 REMARK 3 8 2.3900 - 2.2900 0.97 1450 139 0.1993 0.2065 REMARK 3 9 2.2900 - 2.2000 0.96 1453 139 0.1957 0.2379 REMARK 3 10 2.2000 - 2.1200 0.97 1433 142 0.2055 0.2680 REMARK 3 11 2.1200 - 2.0600 0.96 1434 139 0.2046 0.2456 REMARK 3 12 2.0600 - 2.0000 0.95 1432 140 0.2069 0.2916 REMARK 3 13 2.0000 - 1.9500 0.93 1374 136 0.2088 0.2057 REMARK 3 14 1.9500 - 1.9000 0.89 1329 134 0.2151 0.2311 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.201 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.331 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.83 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 : 0.007 1261 REMARK 3 ANGLE : 0.899 1702 REMARK 3 CHIRALITY : 0.057 179 REMARK 3 PLANARITY : 0.008 224 REMARK 3 DIHEDRAL : 18.736 166 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 7Y7O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.28176 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22303 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 96.6 REMARK 200 DATA REDUNDANCY : 21.10 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.7 REMARK 200 DATA REDUNDANCY IN SHELL : 18.80 REMARK 200 R MERGE FOR SHELL (I) : 0.18400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 14.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE (PH 5.5), 40% REMARK 280 (V/V) PEG 400, 1 MM ZINC SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 287.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.09350 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.09350 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 25.09350 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: 60 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 MET A 0 REMARK 465 GLU A 72 REMARK 465 GLU A 73 REMARK 465 ASP A 74 REMARK 465 GLU A 75 REMARK 465 PRO A 76 REMARK 465 GLU A 77 REMARK 465 ILE A 78 REMARK 465 ASP A 79 REMARK 465 PHE A 80 REMARK 465 SER A 81 REMARK 465 GLY A 82 REMARK 465 LEU A 83 REMARK 465 ASP A 84 REMARK 465 ILE A 85 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 HIS A 130 38.11 -142.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 120 NE2 REMARK 620 2 HIS A 124 NE2 94.0 REMARK 620 3 HIS A 130 NE2 96.6 96.5 REMARK 620 4 CIT A 202 O2 90.1 173.6 87.9 REMARK 620 5 CIT A 202 O5 174.6 88.4 87.9 87.1 REMARK 620 6 CIT A 202 O7 96.4 91.5 164.1 83.1 78.6 REMARK 620 N 1 2 3 4 5 DBREF 7Y7O A 2 155 UNP P67136 YBEY_STAAM 2 155 SEQADV 7Y7O MET A 0 UNP P67136 INITIATING METHIONINE SEQADV 7Y7O ALA A 1 UNP P67136 EXPRESSION TAG SEQADV 7Y7O HIS A 156 UNP P67136 EXPRESSION TAG SEQADV 7Y7O HIS A 157 UNP P67136 EXPRESSION TAG SEQADV 7Y7O HIS A 158 UNP P67136 EXPRESSION TAG SEQADV 7Y7O HIS A 159 UNP P67136 EXPRESSION TAG SEQADV 7Y7O HIS A 160 UNP P67136 EXPRESSION TAG SEQADV 7Y7O HIS A 161 UNP P67136 EXPRESSION TAG SEQRES 1 A 162 MET ALA PHE THR ILE ASP PHE SER ASP HIS THR GLY LEU SEQRES 2 A 162 VAL LYS ASP ALA TRP TYR LYS GLN ILE GLU ASP LEU LEU SEQRES 3 A 162 GLU PHE ALA LYS LYS GLU GLU HIS ILE GLU ASP ASP ALA SEQRES 4 A 162 GLU LEU SER VAL THR PHE VAL ASP LYS GLN GLU ILE GLN SEQRES 5 A 162 GLU ILE ASN ARG THR TYR ARG ASP LYS ASP LYS VAL THR SEQRES 6 A 162 ASP VAL ILE SER PHE ALA LEU GLU GLU ASP GLU PRO GLU SEQRES 7 A 162 ILE ASP PHE SER GLY LEU ASP ILE PRO ARG VAL LEU GLY SEQRES 8 A 162 ASP ILE ILE ILE CYS THR ASP VAL ALA GLN GLU GLN ALA SEQRES 9 A 162 ASN ASN TYR GLY HIS SER PHE GLU ARG GLU LEU GLY PHE SEQRES 10 A 162 LEU ALA LEU HIS GLY PHE LEU HIS LEU LEU GLY TYR ASP SEQRES 11 A 162 HIS MET THR GLU ALA ASP GLU LYS GLU MET PHE GLY ARG SEQRES 12 A 162 GLN ASP THR ILE LEU ASN ALA TYR GLY LEU THR ARG ASP SEQRES 13 A 162 HIS HIS HIS HIS HIS HIS HET ZN A 201 1 HET CIT A 202 13 HET CIT A 203 13 HETNAM ZN ZINC ION HETNAM CIT CITRIC ACID FORMUL 2 ZN ZN 2+ FORMUL 3 CIT 2(C6 H8 O7) FORMUL 5 HOH *54(H2 O) HELIX 1 AA1 LYS A 14 GLU A 32 1 19 HELIX 2 AA2 ASP A 46 ASP A 59 1 14 HELIX 3 AA3 THR A 96 GLY A 107 1 12 HELIX 4 AA4 SER A 109 LEU A 126 1 18 HELIX 5 AA5 THR A 132 TYR A 150 1 19 HELIX 6 AA6 ARG A 154 HIS A 159 5 6 SHEET 1 AA1 4 PHE A 2 ASP A 8 0 SHEET 2 AA1 4 ALA A 38 VAL A 45 1 O PHE A 44 N SER A 7 SHEET 3 AA1 4 ARG A 87 CYS A 95 1 O LEU A 89 N GLU A 39 SHEET 4 AA1 4 VAL A 66 ALA A 70 -1 N PHE A 69 O ASP A 91 LINK NE2 HIS A 120 ZN ZN A 201 1555 1555 2.22 LINK NE2 HIS A 124 ZN ZN A 201 1555 1555 2.22 LINK NE2 HIS A 130 ZN ZN A 201 1555 1555 2.23 LINK ZN ZN A 201 O2 CIT A 202 1555 1555 2.06 LINK ZN ZN A 201 O5 CIT A 202 1555 1555 2.19 LINK ZN ZN A 201 O7 CIT A 202 1555 1555 2.14 CRYST1 100.663 100.663 50.187 90.00 90.00 120.00 P 63 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 0.009934 0.005735 0.000000 0.00000 SCALE2 0.000000 0.011471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019925 0.00000