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 MASTER 263 0 0 12 6 0 0 6 2069 2 0 20 END