HEADER HYDROLASE 14-OCT-12 2M00 TITLE SOLUTION STRUCTURE OF STAPHYLOCOCCAL NUCLEASE E43S MUTANT IN THE TITLE 2 PRESENCE OF SSDNA AND CD2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE; COMPND 5 EC: 3.1.31.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 196620; SOURCE 4 STRAIN: MW2; SOURCE 5 GENE: NUC, MW0769; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-3D KEYWDS HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.XIE,Y.FENG,L.SHAN,J.WANG REVDAT 4 15-MAY-24 2M00 1 REMARK REVDAT 3 14-JUN-23 2M00 1 REMARK SEQADV REVDAT 2 03-APR-13 2M00 1 JRNL REVDAT 1 06-MAR-13 2M00 0 JRNL AUTH T.XIE,Y.FENG,L.SHAN,J.WANG JRNL TITL MODELING OF THE [E43S]SNASE-SSDNA-CD(2+) COMPLEX: STRUCTURAL JRNL TITL 2 INSIGHT INTO THE ACTION OF NUCLEASE ON SSDNA. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 532 103 2013 JRNL REFN ISSN 0003-9861 JRNL PMID 23416741 JRNL DOI 10.1016/J.ABB.2013.02.003 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, CNS REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M00 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000103036. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 305 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 210 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0-1.5 MM [U-13C; U-15N] REMARK 210 PROTEIN, 50 MM SODIUM PHOSPHATE, REMARK 210 150 MM POTASSIUM CHLORIDE, 10 MM REMARK 210 CDCL2, 0.002 W/V SODIUM AZIDE, REMARK 210 1.5-2.25 MM 8-MER SSDNA(5'- REMARK 210 CACTTCAT-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCO; REMARK 210 3D HN(CA)CO; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HBHANH; REMARK 210 3D 1H-15N TOCSY; 3D HCCH-TOCSY; REMARK 210 3D HCCH-COSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX, CNS REMARK 210 METHOD USED : MOLECULAR DYNAMICS, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 75 HE2 HIS A 121 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 1 THR A 2 96.11 74.49 REMARK 500 1 LYS A 5 105.56 70.08 REMARK 500 1 LEU A 7 -171.88 60.39 REMARK 500 1 ASP A 19 -161.50 -162.40 REMARK 500 1 LEU A 37 -61.48 68.13 REMARK 500 1 THR A 44 91.49 -49.04 REMARK 500 1 LYS A 45 -31.20 154.29 REMARK 500 1 GLU A 52 164.35 72.81 REMARK 500 1 GLU A 57 169.31 59.92 REMARK 500 1 ASN A 119 87.23 -160.07 REMARK 500 1 GLU A 142 96.08 -50.44 REMARK 500 1 ASP A 143 -76.42 -166.25 REMARK 500 2 LYS A 5 57.30 -93.12 REMARK 500 2 ILE A 15 -60.38 -106.44 REMARK 500 2 ASP A 19 -163.68 -161.28 REMARK 500 2 LEU A 36 147.67 76.72 REMARK 500 2 LEU A 37 -149.04 -175.69 REMARK 500 2 SER A 43 96.94 -61.77 REMARK 500 2 LYS A 45 79.67 -155.60 REMARK 500 2 HIS A 46 -67.32 -99.93 REMARK 500 2 ASN A 119 26.01 -160.40 REMARK 500 2 SER A 141 43.10 -75.88 REMARK 500 2 ASP A 146 -72.82 -176.29 REMARK 500 2 SER A 147 84.88 64.81 REMARK 500 3 ILE A 15 -60.63 -106.31 REMARK 500 3 ILE A 18 -61.95 -90.13 REMARK 500 3 PRO A 47 88.23 -60.79 REMARK 500 3 PRO A 56 14.24 -69.58 REMARK 500 3 TYR A 113 94.25 -62.26 REMARK 500 3 ASN A 119 -6.15 -159.39 REMARK 500 3 LEU A 137 -176.23 -66.87 REMARK 500 4 LYS A 5 93.77 -171.67 REMARK 500 4 ILE A 15 -60.16 -102.66 REMARK 500 4 ASP A 19 -153.51 -157.27 REMARK 500 4 THR A 44 -34.64 70.63 REMARK 500 4 LYS A 53 -57.67 -139.48 REMARK 500 4 TYR A 54 5.32 -177.37 REMARK 500 4 GLU A 57 -58.65 69.72 REMARK 500 4 ASN A 118 76.68 -66.00 REMARK 500 4 ASN A 119 25.29 -159.32 REMARK 500 4 SER A 141 -63.71 -91.52 REMARK 500 4 ALA A 145 -51.54 70.31 REMARK 500 5 LYS A 5 -61.83 -123.38 REMARK 500 5 LYS A 6 -178.53 73.06 REMARK 500 5 LEU A 7 -160.90 61.87 REMARK 500 5 ASP A 19 -152.25 -160.29 REMARK 500 5 PRO A 42 43.67 -72.98 REMARK 500 5 LYS A 48 -53.04 -139.19 REMARK 500 5 ASN A 118 84.17 -69.78 REMARK 500 5 LEU A 137 -171.43 -62.31 REMARK 500 REMARK 500 THIS ENTRY HAS 195 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 ARG A 126 0.10 SIDE CHAIN REMARK 500 9 ARG A 87 0.09 SIDE CHAIN REMARK 500 12 ARG A 35 0.10 SIDE CHAIN REMARK 500 17 ARG A 87 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18788 RELATED DB: BMRB DBREF 2M00 A 1 149 UNP Q8NXI6 NUC_STAAW 80 228 SEQADV 2M00 SER A 43 UNP Q8NXI6 GLU 122 ENGINEERED MUTATION SEQRES 1 A 149 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 A 149 LEU ILE LYS ALA ILE ASP GLY ASP THR VAL LYS LEU MET SEQRES 3 A 149 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 A 149 ASP THR PRO SER THR LYS HIS PRO LYS LYS GLY VAL GLU SEQRES 5 A 149 LYS TYR GLY PRO GLU ALA SER ALA PHE THR LYS LYS MET SEQRES 6 A 149 VAL GLU ASN ALA LYS LYS ILE GLU VAL GLU PHE ASP LYS SEQRES 7 A 149 GLY GLN ARG THR ASP LYS TYR GLY ARG GLY LEU ALA TYR SEQRES 8 A 149 ILE TYR ALA ASP GLY LYS MET VAL ASN GLU ALA LEU VAL SEQRES 9 A 149 ARG GLN GLY LEU ALA LYS VAL ALA TYR VAL TYR LYS PRO SEQRES 10 A 149 ASN ASN THR HIS GLU GLN LEU LEU ARG LYS SER GLU ALA SEQRES 11 A 149 GLN ALA LYS LYS GLU LYS LEU ASN ILE TRP SER GLU ASP SEQRES 12 A 149 ASN ALA ASP SER GLY GLN HELIX 1 1 PRO A 56 ALA A 69 1 14 HELIX 2 2 VAL A 99 GLN A 106 1 8 HELIX 3 3 HIS A 121 GLU A 135 1 15 SHEET 1 A 7 LYS A 97 MET A 98 0 SHEET 2 A 7 GLY A 88 ALA A 94 -1 N ALA A 94 O LYS A 97 SHEET 3 A 7 ILE A 72 PHE A 76 -1 N GLU A 73 O TYR A 93 SHEET 4 A 7 HIS A 8 ALA A 17 -1 N GLU A 10 O VAL A 74 SHEET 5 A 7 THR A 22 TYR A 27 -1 O MET A 26 N THR A 13 SHEET 6 A 7 GLN A 30 ARG A 35 -1 O GLN A 30 N TYR A 27 SHEET 7 A 7 GLY A 88 ALA A 94 1 O GLY A 88 N THR A 33 SHEET 1 B 2 VAL A 39 ASP A 40 0 SHEET 2 B 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 CISPEP 1 LYS A 116 PRO A 117 1 7.82 CISPEP 2 LYS A 116 PRO A 117 2 4.91 CISPEP 3 LYS A 116 PRO A 117 3 5.60 CISPEP 4 LYS A 116 PRO A 117 4 2.53 CISPEP 5 LYS A 116 PRO A 117 5 3.30 CISPEP 6 LYS A 116 PRO A 117 6 3.27 CISPEP 7 LYS A 116 PRO A 117 7 2.64 CISPEP 8 LYS A 116 PRO A 117 8 -0.22 CISPEP 9 LYS A 116 PRO A 117 9 -0.43 CISPEP 10 LYS A 116 PRO A 117 10 1.00 CISPEP 11 LYS A 116 PRO A 117 11 0.45 CISPEP 12 LYS A 116 PRO A 117 12 5.85 CISPEP 13 LYS A 116 PRO A 117 13 -1.34 CISPEP 14 LYS A 116 PRO A 117 14 1.87 CISPEP 15 LYS A 116 PRO A 117 15 0.67 CISPEP 16 LYS A 116 PRO A 117 16 4.67 CISPEP 17 LYS A 116 PRO A 117 17 1.38 CISPEP 18 LYS A 116 PRO A 117 18 0.87 CISPEP 19 LYS A 116 PRO A 117 19 2.56 CISPEP 20 LYS A 116 PRO A 117 20 -1.50 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1