HEADER DNA BINDING PROTEIN 01-JUL-10 2XIU TITLE HIGH RESOLUTION STRUCTURE OF MTSL-TAGGED CYLR2. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYLR2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYTOLYSIN REPRESSOR 2; COMPND 5 ENGINEERED: YES; COMPND 6 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 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 6 23-OCT-24 2XIU 1 REMARK REVDAT 5 20-DEC-23 2XIU 1 REMARK REVDAT 4 22-MAY-19 2XIU 1 REMARK REVDAT 3 06-MAR-19 2XIU 1 REMARK LINK REVDAT 2 18-MAY-11 2XIU 1 JRNL REMARK SEQADV SEQRES REVDAT 2 2 1 HET MODRES HETNAM HETSYN REVDAT 2 3 1 FORMUL LINK SITE ATOM REVDAT 2 4 1 ANISOU TER HETATM CONECT REVDAT 2 5 1 MASTER REVDAT 1 09-FEB-11 2XIU 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 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) : 0.147 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.142 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.072 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1318 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 25981 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)) : 0.131 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 4.996 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1114 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 22297 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1064 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1216.1 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1125.4 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 19 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 12002 REMARK 3 NUMBER OF RESTRAINTS : 16036 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.367 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.063 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.051 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.030 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.053 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.043 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 2XIU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1290044397. 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) : 0.8 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 : 25981 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 44.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.070 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.38 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.01 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 (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 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 20.48600 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 10.24300 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 30.72900 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: 1800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.6 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 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 GLU B 66 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 MET A 1 CE REMARK 470 LYS A 12 CD CE NZ REMARK 470 LYS A 38 CE NZ REMARK 470 MET B 1 CE REMARK 470 LYS B 12 CE NZ REMARK 470 LYS B 14 CE NZ 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 LYS B 12 CG LYS B 12 CD 1.164 REMARK 500 REMARK 500 REMARK: NULL 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 LYS B 12 CB - CG - CD ANGL. DEV. = -40.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTN A 1055 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTN B 1055 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: 1UTX RELATED DB: PDB REMARK 900 REGULATION OF CYTOLYSIN EXPRESSION BY ENTEROCOCCUS FAECALIS: ROLE REMARK 900 OF CYLR2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAINS A AND B HAVE MICROHETEROGENEITY AT CYS 55, WHICH WAS AN REMARK 999 ENGINEERED MUTATION FROM THR, PARTIALLY REACTED WITH REMARK 999 S-(2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL REMARK 999 METHANESULFONOTHIOATE (MTSL) TO GIVE THE MODIFIED RESIDUE REMARK 999 THIOMETHYL-3-TETRAMETHYL PYRROLINE-1-OXYL CYSTEINE. DBREF 2XIU A 1 66 UNP Q8VL32 Q8VL32_ENTFA 1 66 DBREF 2XIU B 1 66 UNP Q8VL32 Q8VL32_ENTFA 1 66 SEQADV 2XIU CYS A 55 UNP Q8VL32 THR 55 ENGINEERED MUTATION SEQADV 2XIU 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 MTN A1055 12 HET GOL B1001 6 HET MTN B1055 12 HETNAM MTN S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3- HETNAM 2 MTN YL)METHYL] METHANESULFONOTHIOATE HETNAM GOL GLYCEROL HETSYN MTN MTSL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MTN 2(C10 H18 N O3 S2) FORMUL 4 GOL C3 H8 O3 FORMUL 6 HOH *129(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 2 ASN B 4 0 SHEET 2 BA 2 PHE B 61 TRP B 63 -1 O GLN B 62 N ILE B 3 LINK SG ACYS A 55 S1 MTN A1055 1555 1555 2.09 LINK SG ACYS B 55 S1 MTN B1055 1555 1555 2.06 SITE 1 AC1 5 ALA A 22 LEU A 23 HOH A2050 LEU B 45 SITE 2 AC1 5 HOH B2036 SITE 1 AC2 3 ASN A 54 CYS A 55 ASP A 59 SITE 1 AC3 4 LYS B 12 ASN B 54 CYS B 55 ASP B 59 CRYST1 63.353 63.353 40.972 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 0.015785 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024407 0.00000