HEADER HYDROLASE 21-OCT-11 2LKV TITLE STAPHYLOCOCCAL NUCLEASE PHS VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 80-228; COMPND 5 SYNONYM: TNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE; COMPND 6 EC: 3.1.31.1; COMPND 7 ENGINEERED: YES; COMPND 8 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: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET KEYWDS HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.MATZAPETAKIS,T.M.PAIS,P.LAMOSA,D.L.TURNER,H.SANTOS REVDAT 2 01-MAY-24 2LKV 1 REMARK SEQADV REVDAT 1 12-SEP-12 2LKV 0 JRNL AUTH T.M.PAIS,P.LAMOSA,M.MATZAPETAKIS,D.L.TURNER,H.SANTOS JRNL TITL MANNOSYLGLYCERATE STABILIZES STAPHYLOCOCCAL NUCLEASE WITH JRNL TITL 2 RESTRICTION OF SLOW BETA-SHEET MOTIONS. JRNL REF PROTEIN SCI. V. 21 1126 2012 JRNL REFN ISSN 0961-8368 JRNL PMID 22619184 JRNL DOI 10.1002/PRO.2100 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CARA 1.8.4, CNS 1.1, CYANA 2.1 REMARK 3 AUTHORS : KELLER AND WUTHRICH (CARA), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS), GUNTERT, MUMENTHALER REMARK 3 AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL STRUCTURES WERE CALCULATED REMARK 3 USING THE ATNOS-CANDID MODULE OF UNIO EMPLOYING CYANA. THE UNIO REMARK 3 DERIVED CONSTANTS WERE INTRODUCED TO CNS USING THE RECOORD REMARK 3 SCRIPTS FOR EXPLICIT WATER REFINEMENT. REMARK 4 REMARK 4 2LKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000102505. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310.00 REMARK 210 PH : 5.50 REMARK 210 IONIC STRENGTH : 0.060 REMARK 210 PRESSURE : 1.00 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-13C; U-15N] SNASE PHS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC/HMQC; 3D 1H-13C REMARK 210 NOESY; 2D 1H-15N HSQC/HMQC; 3D REMARK 210 1H-15N NOESY; 3D CBCA(CO)NH; REMARK 210 CBCGCGHD (HBCBCGCDHD); HCCH REMARK 210 TOCSY (HC_CH.TOCSY); 3D HNCACB; REMARK 210 3D HBHA(CO)NH; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.1, REMARK 210 CCPNMR_ENTRY_COMPLETION_INTERFACE 2.1, TOPSPIN 2.1, UNIO 2.0, REMARK 210 CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 OD2 ASP A 21 HG1 THR A 41 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 5 ASN A 144 N ASN A 144 CA -0.123 REMARK 500 8 TYR A 91 CB TYR A 91 CG -0.092 REMARK 500 9 LEU A 89 N LEU A 89 CA -0.121 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 LYS A 6 76.84 -100.46 REMARK 500 1 LYS A 16 118.44 -164.80 REMARK 500 1 LYS A 45 -143.59 -87.91 REMARK 500 1 LYS A 48 -84.33 -129.79 REMARK 500 1 LYS A 53 48.63 -64.51 REMARK 500 1 TYR A 54 34.58 -75.08 REMARK 500 1 LYS A 84 -79.53 56.11 REMARK 500 1 ALA A 112 -159.29 -102.96 REMARK 500 1 TYR A 113 113.45 -168.41 REMARK 500 1 VAL A 114 -60.30 -90.68 REMARK 500 1 LYS A 116 98.69 -60.09 REMARK 500 1 ASN A 119 23.11 -167.03 REMARK 500 1 LYS A 136 83.28 77.76 REMARK 500 1 ASN A 138 -89.70 41.88 REMARK 500 1 ALA A 145 -68.34 -133.52 REMARK 500 1 SER A 147 31.73 -156.23 REMARK 500 2 THR A 2 -71.48 -90.33 REMARK 500 2 SER A 3 139.81 64.87 REMARK 500 2 LYS A 5 41.27 -108.15 REMARK 500 2 ILE A 18 -71.23 -97.38 REMARK 500 2 THR A 22 118.46 170.86 REMARK 500 2 LYS A 48 -59.07 -165.63 REMARK 500 2 VAL A 51 69.10 65.85 REMARK 500 2 GLU A 52 170.39 -44.64 REMARK 500 2 LYS A 53 64.38 -67.44 REMARK 500 2 ASP A 77 -169.80 -75.73 REMARK 500 2 ASP A 83 -106.31 -119.38 REMARK 500 2 ASP A 95 -1.26 78.32 REMARK 500 2 LYS A 116 107.73 -55.97 REMARK 500 2 ASN A 119 27.41 -172.80 REMARK 500 2 LYS A 136 67.29 78.73 REMARK 500 2 ASN A 138 -78.32 -30.02 REMARK 500 2 SER A 147 -74.67 -170.76 REMARK 500 3 LYS A 5 131.27 61.77 REMARK 500 3 LYS A 16 122.07 -174.02 REMARK 500 3 THR A 22 124.86 157.64 REMARK 500 3 LYS A 53 94.85 -66.11 REMARK 500 3 TYR A 54 36.50 -86.41 REMARK 500 3 ASP A 83 -125.41 -108.16 REMARK 500 3 LYS A 84 -75.38 -25.57 REMARK 500 3 ALA A 112 -163.67 -103.71 REMARK 500 3 VAL A 114 -65.76 -90.47 REMARK 500 3 LYS A 116 109.89 -54.41 REMARK 500 3 ASN A 119 23.58 -163.03 REMARK 500 3 LYS A 136 68.01 78.04 REMARK 500 3 ASN A 138 -89.52 46.64 REMARK 500 3 GLU A 142 -77.94 -63.98 REMARK 500 3 ASP A 143 -36.75 -177.66 REMARK 500 3 ALA A 145 -72.20 -86.51 REMARK 500 3 SER A 147 -39.19 174.91 REMARK 500 REMARK 500 THIS ENTRY HAS 167 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 3 ARG A 35 0.10 SIDE CHAIN REMARK 500 4 ARG A 35 0.14 SIDE CHAIN REMARK 500 5 ARG A 81 0.09 SIDE CHAIN REMARK 500 6 ARG A 35 0.09 SIDE CHAIN REMARK 500 7 ARG A 81 0.07 SIDE CHAIN REMARK 500 8 ARG A 35 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18013 RELATED DB: BMRB DBREF 2LKV A 1 149 UNP Q8NXI6 NUC_STAAW 80 228 SEQADV 2LKV GLY A 117 UNP Q8NXI6 PRO 196 ENGINEERED MUTATION SEQADV 2LKV ALA A 128 UNP Q8NXI6 SER 207 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 GLU 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 GLY SEQRES 10 A 149 ASN ASN THR HIS GLU GLN LEU LEU ARG LYS ALA 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 TYR A 54 ALA A 69 1 16 HELIX 2 2 VAL A 99 GLN A 106 1 8 HELIX 3 3 HIS A 121 LYS A 136 1 16 HELIX 4 4 LEU A 137 GLU A 142 5 6 SHEET 1 A 8 THR A 82 ASP A 83 0 SHEET 2 A 8 LYS A 97 MET A 98 0 SHEET 3 A 8 GLN A 30 LEU A 36 0 SHEET 4 A 8 THR A 22 TYR A 27 -1 N VAL A 23 O PHE A 34 SHEET 5 A 8 HIS A 8 ALA A 17 -1 N LYS A 16 O LYS A 24 SHEET 6 A 8 ILE A 72 PHE A 76 -1 O ILE A 72 N ALA A 12 SHEET 7 A 8 ARG A 87 ALA A 94 -1 O TYR A 91 N GLU A 75 SHEET 8 A 8 LYS A 97 MET A 98 -1 O LYS A 97 N ALA A 94 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 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