HEADER DNA BINDING PROTEIN 13-FEB-04 1SD6 TITLE CRYSTAL STRUCTURE OF NATIVE MECI AT 2.65 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHICILLIN RESISTANCE REGULATORY PROTEIN MECI; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MECI; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: MECI, SA0040; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3 KEYWDS BLAI, MECI, REPRESSOR, METHICILLIN, B-LACTAM, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.K.SAFO,Q.ZHAO,F.N.MUSAYEV,H.ROBINSON,N.SCARSDALE,G.L.ARCHER REVDAT 5 14-FEB-24 1SD6 1 SEQADV REVDAT 4 11-OCT-17 1SD6 1 REMARK REVDAT 3 24-FEB-09 1SD6 1 VERSN REVDAT 2 29-MAR-05 1SD6 1 JRNL REVDAT 1 24-FEB-04 1SD6 0 JRNL AUTH M.K.SAFO,Q.ZHAO,T.-P.KO,F.N.MUSAYEV,H.ROBINSON,N.SCARSDALE, JRNL AUTH 2 A.H.-J.WANG,G.L.ARCHER JRNL TITL CRYSTAL STRUCTURES OF THE BLAI REPRESSOR FROM STAPHYLOCOCCUS JRNL TITL 2 AUREUS AND ITS COMPLEX WITH DNA: INSIGHTS INTO JRNL TITL 3 TRANSCRIPTIONAL REGULATION OF THE BLA AND MEC OPERONS JRNL REF J.BACTERIOL. V. 187 1833 2005 JRNL REFN ISSN 0021-9193 JRNL PMID 15716455 JRNL DOI 10.1128/JB.187.5.1833-1844.2005 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.500 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 91660.170 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 9347 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 439 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1353 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 77 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2010 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.14000 REMARK 3 B22 (A**2) : 1.65000 REMARK 3 B33 (A**2) : -5.79000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM SIGMAA (A) : 0.55 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.860 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 48.11 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SD6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MSC CONFOCAL MIRROR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9418 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 36.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, SODIUM CACODYLATE, MAGNESIUM REMARK 280 ACETATE , PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 31.85550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.79750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.37400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.79750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.85550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.37400 REMARK 290 SMTRY3 4 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS THE BIOLOGICAL HOMODIMER 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 ASN A 3 REMARK 465 LYS A 4 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 ASN B 3 REMARK 465 LYS B 4 REMARK 465 LYS B 123 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 TYR A 6 109.16 99.39 REMARK 500 MET A 21 -61.66 -95.71 REMARK 500 LYS A 23 -54.45 66.23 REMARK 500 LYS A 61 -153.15 -103.06 REMARK 500 LYS A 62 51.51 -157.14 REMARK 500 ASN A 64 -142.22 65.17 REMARK 500 MET B 21 -74.82 -72.21 REMARK 500 LYS B 23 -48.78 87.76 REMARK 500 ASP B 39 56.82 -93.86 REMARK 500 ASN B 64 -142.80 77.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SD7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A SEMET DERIVATIVE OF MECI AT 2.65 A REMARK 900 RELATED ID: 1SD4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A SEMET DERIVATIVE OF BLAI AT 2.0 A DBREF 1SD6 A 1 123 UNP P68262 MECI_STAAU 1 123 DBREF 1SD6 B 1 123 UNP P68262 MECI_STAAU 1 123 SEQADV 1SD6 GLU A 107 UNP P68262 ASP 107 CONFLICT SEQADV 1SD6 GLU B 107 UNP P68262 ASP 107 CONFLICT SEQRES 1 A 123 MET ASP ASN LYS THR TYR GLU ILE SER SER ALA GLU TRP SEQRES 2 A 123 GLU VAL MET ASN ILE ILE TRP MET LYS LYS TYR ALA SER SEQRES 3 A 123 ALA ASN ASN ILE ILE GLU GLU ILE GLN MET GLN LYS ASP SEQRES 4 A 123 TRP SER PRO LYS THR ILE ARG THR LEU ILE THR ARG LEU SEQRES 5 A 123 TYR LYS LYS GLY PHE ILE ASP ARG LYS LYS ASP ASN LYS SEQRES 6 A 123 ILE PHE GLN TYR TYR SER LEU VAL GLU GLU SER ASP ILE SEQRES 7 A 123 LYS TYR LYS THR SER LYS ASN PHE ILE ASN LYS VAL TYR SEQRES 8 A 123 LYS GLY GLY PHE ASN SER LEU VAL LEU ASN PHE VAL GLU SEQRES 9 A 123 LYS GLU GLU LEU SER GLN ASP GLU ILE GLU GLU LEU ARG SEQRES 10 A 123 ASN ILE LEU ASN LYS LYS SEQRES 1 B 123 MET ASP ASN LYS THR TYR GLU ILE SER SER ALA GLU TRP SEQRES 2 B 123 GLU VAL MET ASN ILE ILE TRP MET LYS LYS TYR ALA SER SEQRES 3 B 123 ALA ASN ASN ILE ILE GLU GLU ILE GLN MET GLN LYS ASP SEQRES 4 B 123 TRP SER PRO LYS THR ILE ARG THR LEU ILE THR ARG LEU SEQRES 5 B 123 TYR LYS LYS GLY PHE ILE ASP ARG LYS LYS ASP ASN LYS SEQRES 6 B 123 ILE PHE GLN TYR TYR SER LEU VAL GLU GLU SER ASP ILE SEQRES 7 B 123 LYS TYR LYS THR SER LYS ASN PHE ILE ASN LYS VAL TYR SEQRES 8 B 123 LYS GLY GLY PHE ASN SER LEU VAL LEU ASN PHE VAL GLU SEQRES 9 B 123 LYS GLU GLU LEU SER GLN ASP GLU ILE GLU GLU LEU ARG SEQRES 10 B 123 ASN ILE LEU ASN LYS LYS FORMUL 3 HOH *59(H2 O) HELIX 1 1 SER A 9 LYS A 23 1 15 HELIX 2 2 ALA A 27 GLN A 35 1 9 HELIX 3 3 SER A 41 LYS A 55 1 15 HELIX 4 4 GLU A 74 TYR A 91 1 18 HELIX 5 5 GLY A 94 GLU A 106 1 13 HELIX 6 6 SER A 109 LYS A 122 1 14 HELIX 7 7 SER B 9 LYS B 23 1 15 HELIX 8 8 SER B 26 MET B 36 1 11 HELIX 9 9 SER B 41 LYS B 55 1 15 HELIX 10 10 GLU B 74 TYR B 91 1 18 HELIX 11 11 GLY B 93 GLU B 106 1 14 HELIX 12 12 SER B 109 LYS B 122 1 14 SHEET 1 A 3 ALA A 25 SER A 26 0 SHEET 2 A 3 GLN A 68 SER A 71 -1 O TYR A 69 N ALA A 25 SHEET 3 A 3 ILE A 58 ARG A 60 -1 N ASP A 59 O TYR A 70 SHEET 1 B 3 TYR B 24 ALA B 25 0 SHEET 2 B 3 PHE B 67 SER B 71 -1 O TYR B 69 N ALA B 25 SHEET 3 B 3 ILE B 58 LYS B 62 -1 N LYS B 61 O GLN B 68 CRYST1 63.711 72.748 73.595 90.00 90.00 90.00 P 21 21 21 8 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 0.015696 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013588 0.00000