HEADER OXIDOREDUCTASE 20-DEC-07 3BQH TITLE STRUCTURE OF THE CENTRAL DOMAIN (MSRA) OF NEISSERIA MENINGITIDIS PILB TITLE 2 (OXIDIZED FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA/MSRB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MSRA DOMAIN, PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA, COMPND 5 UNP RESIDUES 197-389; COMPND 6 SYNONYM: PILB; COMPND 7 EC: 1.8.4.11; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 122587; SOURCE 4 STRAIN: Z2491; SOURCE 5 GENE: PILB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BE002; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSKPILBMSRA KEYWDS PILB, METHIONINE SULFOXIDE REDUCTASE A, OXIDIZED FORM, ELECTRON KEYWDS 2 TRANSPORT, MULTIFUNCTIONAL ENZYME, OXIDOREDUCTASE, REDOX-ACTIVE KEYWDS 3 CENTER, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.M.RANAIVOSON,B.KAUFFMANN,F.FAVIER REVDAT 6 20-NOV-24 3BQH 1 REMARK REVDAT 5 01-NOV-23 3BQH 1 REMARK REVDAT 4 13-JUL-11 3BQH 1 VERSN REVDAT 3 24-FEB-09 3BQH 1 VERSN REVDAT 2 18-MAR-08 3BQH 1 JRNL REVDAT 1 19-FEB-08 3BQH 0 JRNL AUTH F.M.RANAIVOSON,M.ANTOINE,B.KAUFFMANN,S.BOSCHI-MULLER, JRNL AUTH 2 A.AUBRY,G.BRANLANT,F.FAVIER JRNL TITL A STRUCTURAL ANALYSIS OF THE CATALYTIC MECHANISM OF JRNL TITL 2 METHIONINE SULFOXIDE REDUCTASE A FROM NEISSERIA MENINGITIDIS JRNL REF J.MOL.BIOL. V. 377 268 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18255097 JRNL DOI 10.1016/J.JMB.2008.01.021 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 234527.234 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 10360 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) : 0.193 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 513 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1619 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 77 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1303 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.70000 REMARK 3 B22 (A**2) : 3.08000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.14 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) : 0.25 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) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.650 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) : 1.920 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.560 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.080 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.370 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 60.94 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ACT.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ACT.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BQH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045840. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.89 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10452 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.35800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3BQE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 21.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 VOLUME OF 30% PEG 4000, 0.2M REMARK 280 AMMONIUM SULFATE,0.1M NA ACETATE PH 4.6, MIXED WITH 1 VOLUME OF REMARK 280 50MM TRIS HCL, 2MM EDTA PH 8, 10MG/ML PROTEIN PRIORLY OXIDIZED, REMARK 280 MICROBATCH-UNDER-OIL, TEMPERATURE 293K 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 21.75000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.80000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 HIS A 350 REMARK 465 ILE A 351 REMARK 465 ASP A 352 REMARK 465 GLY A 362 REMARK 465 LYS A 363 REMARK 465 THR A 364 REMARK 465 LYS A 365 REMARK 465 THR A 366 REMARK 465 ALA A 367 REMARK 465 PRO A 368 REMARK 465 GLN A 369 REMARK 465 GLY A 370 REMARK 465 LYS A 371 REMARK 465 GLY A 372 REMARK 465 PHE A 373 REMARK 465 ASP A 374 REMARK 465 ALA A 375 REMARK 465 ALA A 376 REMARK 465 THR A 377 REMARK 465 TYR A 378 REMARK 465 LYS A 379 REMARK 465 LYS A 380 REMARK 465 PRO A 381 REMARK 465 SER A 382 REMARK 465 ASP A 383 REMARK 465 ALA A 384 REMARK 465 GLU A 385 REMARK 465 LEU A 386 REMARK 465 LYS A 387 REMARK 465 ARG A 388 REMARK 465 THR A 389 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BQE RELATED DB: PDB REMARK 900 THE SAME PROTEIN, REDUCED FORM REMARK 900 RELATED ID: 3BQF RELATED DB: PDB REMARK 900 C207S MUTANT OF THE SAME PROTEIN, COMPLEX WITH A SUBSTRATE REMARK 900 RELATED ID: 3BQG RELATED DB: PDB REMARK 900 THE SAME PROTEIN, SULFENIC ACID FORM DBREF 3BQH A 197 389 UNP Q9JWM8 MSRAB_NEIMA 197 389 SEQRES 1 A 193 ASN THR ARG THR ILE TYR LEU ALA GLY GLY CYS PHE TRP SEQRES 2 A 193 GLY LEU GLU ALA TYR PHE GLN ARG ILE ASP GLY VAL VAL SEQRES 3 A 193 ASP ALA VAL SER GLY TYR ALA ASN GLY ASN THR LYS ASN SEQRES 4 A 193 PRO SER TYR GLU ASP VAL SER TYR ARG HIS THR GLY HIS SEQRES 5 A 193 ALA GLU THR VAL LYS VAL THR TYR ASP ALA ASP LYS LEU SEQRES 6 A 193 SER LEU ASP ASP ILE LEU GLN TYR PHE PHE ARG VAL VAL SEQRES 7 A 193 ASP PRO THR SER LEU ASN LYS GLN GLY ASN ASP THR GLY SEQRES 8 A 193 THR GLN TYR ARG SER GLY VAL TYR TYR THR ASP PRO ALA SEQRES 9 A 193 GLU LYS ALA VAL ILE ALA ALA ALA LEU LYS ARG GLU GLN SEQRES 10 A 193 GLN LYS TYR GLN LEU PRO LEU VAL VAL GLU ASN GLU PRO SEQRES 11 A 193 LEU LYS ASN PHE TYR ASP ALA GLU GLU TYR HIS GLN ASP SEQRES 12 A 193 TYR LEU ILE LYS ASN PRO ASN GLY TYR CYS HIS ILE ASP SEQRES 13 A 193 ILE ARG LYS ALA ASP GLU PRO LEU PRO GLY LYS THR LYS SEQRES 14 A 193 THR ALA PRO GLN GLY LYS GLY PHE ASP ALA ALA THR TYR SEQRES 15 A 193 LYS LYS PRO SER ASP ALA GLU LEU LYS ARG THR HET ACT A1000 4 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *76(H2 O) HELIX 1 1 CYS A 207 ARG A 217 1 11 HELIX 2 2 SER A 237 ARG A 244 1 8 HELIX 3 3 SER A 262 VAL A 274 1 13 HELIX 4 4 THR A 277 LYS A 281 5 5 HELIX 5 5 ASP A 298 GLN A 314 1 17 HELIX 6 6 GLU A 334 GLN A 338 5 5 HELIX 7 7 ASP A 339 ASN A 344 1 6 SHEET 1 A 6 GLU A 323 PRO A 326 0 SHEET 2 A 6 SER A 292 TYR A 296 1 N VAL A 294 O GLU A 323 SHEET 3 A 6 THR A 198 GLY A 205 -1 N TYR A 202 O TYR A 295 SHEET 4 A 6 ALA A 249 ASP A 257 -1 O VAL A 254 N ILE A 201 SHEET 5 A 6 VAL A 221 ALA A 229 -1 N VAL A 225 O LYS A 253 SHEET 6 A 6 PHE A 330 ASP A 332 -1 O TYR A 331 N TYR A 228 SSBOND 1 CYS A 207 CYS A 349 1555 1555 2.03 SITE 1 AC1 8 HOH A 58 GLU A 212 ASP A 223 ALA A 224 SITE 2 AC1 8 VAL A 225 ARG A 311 GLN A 338 ASP A 339 CRYST1 43.500 47.600 66.000 90.00 90.00 90.00 P 21 21 21 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 0.022989 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021008 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015152 0.00000