HEADER OXIDOREDUCTASE 07-FEB-06 2FY6 TITLE STRUCTURE OF THE N-TERMINAL DOMAIN OF NEISSERIA MENINGITIDIS PILB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA/MSRB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THIOREDOXIN-LIKE DOMAIN; COMPND 5 EC: 1.8.4.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 122587; SOURCE 4 STRAIN: Z2491; SOURCE 5 GENE: MSRAB, PILB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24C KEYWDS PILB, CYTOCHROME MATURATION PROTEIN, THIOREDOXIN, METHIONINE KEYWDS 2 SULFOXIDE REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.M.RANAIVOSON,B.KAUFFMANN,F.NEIERS,S.BOSCHI-MULLER,G.BRANLANT, AUTHOR 2 F.FAVIER REVDAT 6 13-MAR-24 2FY6 1 REMARK REVDAT 5 18-OCT-17 2FY6 1 REMARK REVDAT 4 13-JUL-11 2FY6 1 VERSN REVDAT 3 24-FEB-09 2FY6 1 VERSN REVDAT 2 09-MAY-06 2FY6 1 JRNL REVDAT 1 04-APR-06 2FY6 0 JRNL AUTH F.M.RANAIVOSON,B.KAUFFMANN,F.NEIERS,J.WU,S.BOSCHI-MULLER, JRNL AUTH 2 S.PANJIKAR,A.AUBRY,G.BRANLANT,F.FAVIER JRNL TITL THE X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF PILB FROM JRNL TITL 2 NEISSERIA MENINGITIDIS REVEALS A THIOREDOXIN-FOLD JRNL REF J.MOL.BIOL. V. 358 443 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16530221 JRNL DOI 10.1016/J.JMB.2006.02.025 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 585795.812 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 10719 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) : 0.182 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1099 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1496 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE : 0.2690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 189 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1110 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.76000 REMARK 3 B22 (A**2) : -0.70000 REMARK 3 B33 (A**2) : -1.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.18 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 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) : 1.280 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.860 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 49.64 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : SULF.PAR REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : SULF.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FY6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000036450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81 REMARK 200 MONOCHROMATOR : TRIANGULAR REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5M AMMONIUM SULFATE, TRIS-HCL 50MM REMARK 280 PH 8.0, 6MG/ML PROTEIN, PH 7.5, MICROBATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.43500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.58450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.43500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.58450 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 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 315 DBREF 2FY6 A 33 175 UNP Q9JWM8 MSRAB_NEIMA 34 176 SEQRES 1 A 143 VAL PRO HIS THR LEU SER THR LEU LYS THR ALA ASP ASN SEQRES 2 A 143 ARG PRO ALA SER VAL TYR LEU LYS LYS ASP LYS PRO THR SEQRES 3 A 143 LEU ILE LYS PHE TRP ALA SER TRP CYS PRO LEU CYS LEU SEQRES 4 A 143 SER GLU LEU GLY GLN THR GLU LYS TRP ALA GLN ASP ALA SEQRES 5 A 143 LYS PHE SER SER ALA ASN LEU ILE THR VAL ALA SER PRO SEQRES 6 A 143 GLY PHE LEU HIS GLU LYS LYS ASP GLY ASP PHE GLN LYS SEQRES 7 A 143 TRP TYR ALA GLY LEU ASN TYR PRO LYS LEU PRO VAL VAL SEQRES 8 A 143 THR ASP ASN GLY GLY THR ILE ALA GLN SER LEU ASN ILE SEQRES 9 A 143 SER VAL TYR PRO SER TRP ALA LEU ILE GLY LYS ASP GLY SEQRES 10 A 143 ASP VAL GLN ARG ILE VAL LYS GLY SER ILE ASN GLU ALA SEQRES 11 A 143 GLN ALA LEU ALA LEU ILE ARG ASP PRO ASN ALA ASP LEU HET CL A 214 1 HET CL A 215 1 HET SO4 A 315 5 HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *154(H2 O) HELIX 1 1 VAL A 33 THR A 39 1 7 HELIX 2 2 PRO A 47 LEU A 52 5 6 HELIX 3 3 CYS A 67 SER A 72 1 6 HELIX 4 4 GLU A 73 ASP A 83 1 11 HELIX 5 5 ALA A 84 SER A 87 5 4 HELIX 6 6 GLY A 106 ALA A 113 1 8 HELIX 7 7 GLY A 128 LEU A 134 1 7 HELIX 8 8 ASN A 160 ASP A 170 1 11 SHEET 1 A 6 LYS A 41 THR A 42 0 SHEET 2 A 6 VAL A 122 THR A 124 -1 O THR A 124 N LYS A 41 SHEET 3 A 6 ASN A 90 ALA A 95 1 N THR A 93 O VAL A 123 SHEET 4 A 6 THR A 58 TRP A 63 1 N LEU A 59 O ASN A 90 SHEET 5 A 6 SER A 141 ILE A 145 -1 O ILE A 145 N THR A 58 SHEET 6 A 6 VAL A 151 LYS A 156 -1 O VAL A 155 N TRP A 142 CISPEP 1 TYR A 139 PRO A 140 0 -0.39 SITE 1 AC1 2 ASN A 135 GLN A 163 SITE 1 AC2 2 GLN A 76 HOH A 437 SITE 1 AC3 7 GLN A 76 LYS A 79 TRP A 80 HOH A 344 SITE 2 AC3 7 HOH A 350 HOH A 426 HOH A 427 CRYST1 56.870 45.169 59.094 90.00 111.87 90.00 C 1 2 1 4 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 0.017580 0.000000 0.007060 0.00000 SCALE2 0.000000 0.022140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018230 0.00000