HEADER DNA BINDING PROTEIN 02-JUL-10 2XJ3 TITLE HIGH RESOLUTION STRUCTURE OF THE T55C MUTANT OF CYLR2. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYLR2 SYNONYM CYTOLYSIN REPRESSOR 2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS DNA BINDING PROTEIN, HTH-DNA BINDING MOTIF, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR T.GRUENE,M.K.CHO,I.KARYAGINA,H.Y.KIM,C.GROSSE,K.GILLER, AUTHOR 2 M.ZWECKSTETTER,S.BECKER REVDAT 5 20-DEC-23 2XJ3 1 REMARK REVDAT 4 22-MAY-19 2XJ3 1 REMARK REVDAT 3 06-MAR-19 2XJ3 1 REMARK REVDAT 2 25-MAY-11 2XJ3 1 JRNL REVDAT 1 09-FEB-11 2XJ3 0 JRNL AUTH T.GRUENE,M.K.CHO,I.KARYAGINA,H.Y.KIM,C.GROSSE,K.GILLER, JRNL AUTH 2 M.ZWECKSTETTER,S.BECKER JRNL TITL INTEGRATED ANALYSIS OF THE CONFORMATION OF A PROTEIN-LINKED JRNL TITL 2 SPIN LABEL BY CRYSTALLOGRAPHY, EPR AND NMR SPECTROSCOPY. JRNL REF J.BIOMOL.NMR V. 49 111 2011 JRNL REFN ISSN 0925-2738 JRNL PMID 21271275 JRNL DOI 10.1007/S10858-011-9471-Y REMARK 2 REMARK 2 RESOLUTION. 1.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.148 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.150 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2359 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 46370 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.136 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.137 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1938 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 38556 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1052 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1204.6 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1072.5 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 22 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11507 REMARK 3 NUMBER OF RESTRAINTS : 14485 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.343 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.069 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.070 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.053 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.036 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.055 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2XJ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1290044402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48194 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 44.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 7.410 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.92 REMARK 200 R MERGE FOR SHELL (I) : 0.20000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.860 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1UTX REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION, 50MM HEPES PH 7.0, REMARK 280 0.2M NACL, VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.60000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.30000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.90000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, THR 55 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, THR 55 TO CYS REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 12 CE NZ REMARK 470 LYS A 38 CD CE NZ REMARK 470 MET B 1 N CB CG SD CE REMARK 470 ILE B 3 CG1 CG2 CD1 REMARK 470 LYS B 12 CE NZ REMARK 470 LYS B 14 CG CD CE NZ REMARK 470 GLN B 62 CD OE1 NE2 REMARK 470 GLN B 64 CD OE1 NE2 REMARK 470 GLU B 66 CA C O CB CG CD OE1 REMARK 470 GLU B 66 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 TYR A 39 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 TYR A 51 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 CYS A 55 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2026 DISTANCE = 6.72 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1067 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1067 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XI8 RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF NATIVE CYLR2 REMARK 900 RELATED ID: 2XIU RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF MTSL-TAGGED CYLR2. REMARK 900 RELATED ID: 1UTX RELATED DB: PDB REMARK 900 REGULATION OF CYTOLYSIN EXPRESSION BY ENTEROCOCCUS FAECALIS: ROLE REMARK 900 OF CYLR2 DBREF 2XJ3 A 1 66 UNP Q8VL32 Q8VL32_ENTFA 1 66 DBREF 2XJ3 B 1 66 UNP Q8VL32 Q8VL32_ENTFA 1 66 SEQADV 2XJ3 CYS A 55 UNP Q8VL32 THR 55 ENGINEERED MUTATION SEQADV 2XJ3 CYS B 55 UNP Q8VL32 THR 55 ENGINEERED MUTATION SEQRES 1 A 66 MET ILE ILE ASN ASN LEU LYS LEU ILE ARG GLU LYS LYS SEQRES 2 A 66 LYS ILE SER GLN SER GLU LEU ALA ALA LEU LEU GLU VAL SEQRES 3 A 66 SER ARG GLN THR ILE ASN GLY ILE GLU LYS ASN LYS TYR SEQRES 4 A 66 ASN PRO SER LEU GLN LEU ALA LEU LYS ILE ALA TYR TYR SEQRES 5 A 66 LEU ASN CYS PRO LEU GLU ASP ILE PHE GLN TRP GLN PRO SEQRES 6 A 66 GLU SEQRES 1 B 66 MET ILE ILE ASN ASN LEU LYS LEU ILE ARG GLU LYS LYS SEQRES 2 B 66 LYS ILE SER GLN SER GLU LEU ALA ALA LEU LEU GLU VAL SEQRES 3 B 66 SER ARG GLN THR ILE ASN GLY ILE GLU LYS ASN LYS TYR SEQRES 4 B 66 ASN PRO SER LEU GLN LEU ALA LEU LYS ILE ALA TYR TYR SEQRES 5 B 66 LEU ASN CYS PRO LEU GLU ASP ILE PHE GLN TRP GLN PRO SEQRES 6 B 66 GLU HET GOL A1067 6 HET GOL B1067 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *151(H2 O) HELIX 1 1 ASN A 5 LYS A 13 1 9 HELIX 2 2 SER A 16 GLU A 25 1 10 HELIX 3 3 SER A 27 LYS A 36 1 10 HELIX 4 4 SER A 42 ASN A 54 1 13 HELIX 5 5 PRO A 56 ILE A 60 1 5 HELIX 6 6 ASN B 5 LYS B 13 1 9 HELIX 7 7 SER B 16 GLU B 25 1 10 HELIX 8 8 SER B 27 LYS B 36 1 10 HELIX 9 9 SER B 42 ASN B 54 1 13 HELIX 10 10 PRO B 56 ILE B 60 1 5 SHEET 1 AA 2 ILE A 2 ASN A 4 0 SHEET 2 AA 2 PHE A 61 TRP A 63 -1 O GLN A 62 N ILE A 3 SHEET 1 BA 2 ILE B 3 ASN B 4 0 SHEET 2 BA 2 PHE B 61 GLN B 62 -1 O GLN B 62 N ILE B 3 SITE 1 AC1 6 LYS A 14 GLN A 62 TRP A 63 HOH A2082 SITE 2 AC1 6 HOH A2083 TYR B 51 SITE 1 AC2 7 ALA A 22 LEU A 23 VAL B 26 LEU B 45 SITE 2 AC2 7 HOH B2071 HOH B2072 HOH B2073 CRYST1 63.450 63.450 41.200 90.00 90.00 90.00 P 41 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 0.015760 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015760 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024272 0.00000