HEADER OXIDOREDUCTASE 20-DEC-07 3BQF TITLE STRUCTURE OF THE CENTRAL DOMAIN (MSRA) OF NEISSERIA MENINGITIDIS PILB TITLE 2 (COMPLEX WITH A SUBSTRATE) 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 A, UNP COMPND 5 RESIDUES 196-389; COMPND 6 SYNONYM: PILB; COMPND 7 EC: 1.8.4.11; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: 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, COMPLEX WITH A SUBSTRATE, KEYWDS 2 ELECTRON TRANSPORT, MULTIFUNCTIONAL ENZYME, OXIDOREDUCTASE, REDOX- KEYWDS 3 ACTIVE CENTER, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.M.RANAIVOSON,B.KAUFFMANN,F.FAVIER REVDAT 7 01-NOV-23 3BQF 1 REMARK REVDAT 6 10-NOV-21 3BQF 1 REMARK SEQADV REVDAT 5 25-OCT-17 3BQF 1 REMARK REVDAT 4 13-JUL-11 3BQF 1 VERSN REVDAT 3 24-FEB-09 3BQF 1 VERSN REVDAT 2 18-MAR-08 3BQF 1 JRNL REVDAT 1 19-FEB-08 3BQF 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. 2.24 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) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 458280.406 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 7169 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) : 0.185 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 694 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1041 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 113 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1341 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : -0.93000 REMARK 3 B33 (A**2) : -0.15000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 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) : 1.330 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.080 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.590 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.360 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.48 REMARK 3 BSOL : 55.55 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 : S_MSO.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 : S_MSO.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BQF 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_1000045838. 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 : 9.0 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 : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.240 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 (%): 26.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 VOLUME OF 30% PEG 550 MME, 0.1M REMARK 280 BICINE PH 9.0, 0.1M NACL, MIXED WITH 1 VOLUME OF 50MM TRIS HCL, REMARK 280 2MM EDTA PH 8, 18MG/ML PROTEIN + 200MM ACMET(R,S)SONHME, 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 21.96650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.27800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.15250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.27800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.96650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.15250 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 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 SSM A 400 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: 3BQG RELATED DB: PDB REMARK 900 THE SAME PROTEIN, SULFENIC ACID FORM REMARK 900 RELATED ID: 3BQH RELATED DB: PDB REMARK 900 THE SAME PROTEIN, OXIDIZED FORM DBREF 3BQF A 196 389 UNP Q9JWM8 MSRAB_NEIMA 196 389 SEQADV 3BQF SER A 207 UNP Q9JWM8 CYS 207 ENGINEERED MUTATION SEQRES 1 A 194 MET ASN THR ARG THR ILE TYR LEU ALA GLY GLY SER PHE SEQRES 2 A 194 TRP GLY LEU GLU ALA TYR PHE GLN ARG ILE ASP GLY VAL SEQRES 3 A 194 VAL ASP ALA VAL SER GLY TYR ALA ASN GLY ASN THR LYS SEQRES 4 A 194 ASN PRO SER TYR GLU ASP VAL SER TYR ARG HIS THR GLY SEQRES 5 A 194 HIS ALA GLU THR VAL LYS VAL THR TYR ASP ALA ASP LYS SEQRES 6 A 194 LEU SER LEU ASP ASP ILE LEU GLN TYR PHE PHE ARG VAL SEQRES 7 A 194 VAL ASP PRO THR SER LEU ASN LYS GLN GLY ASN ASP THR SEQRES 8 A 194 GLY THR GLN TYR ARG SER GLY VAL TYR TYR THR ASP PRO SEQRES 9 A 194 ALA GLU LYS ALA VAL ILE ALA ALA ALA LEU LYS ARG GLU SEQRES 10 A 194 GLN GLN LYS TYR GLN LEU PRO LEU VAL VAL GLU ASN GLU SEQRES 11 A 194 PRO LEU LYS ASN PHE TYR ASP ALA GLU GLU TYR HIS GLN SEQRES 12 A 194 ASP TYR LEU ILE LYS ASN PRO ASN GLY TYR CYS HIS ILE SEQRES 13 A 194 ASP ILE ARG LYS ALA ASP GLU PRO LEU PRO GLY LYS THR SEQRES 14 A 194 LYS THR ALA PRO GLN GLY LYS GLY PHE ASP ALA ALA THR SEQRES 15 A 194 TYR LYS LYS PRO SER ASP ALA GLU LEU LYS ARG THR HET SSM A 400 14 HETNAM SSM (2S)-2-(ACETYLAMINO)-N-METHYL-4-[(S)- HETNAM 2 SSM METHYLSULFINYL]BUTANAMIDE FORMUL 2 SSM C8 H16 N2 O3 S FORMUL 3 HOH *82(H2 O) HELIX 1 1 SER 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 288 TYR A 290 5 3 HELIX 5 5 ASP A 298 ALA A 300 5 3 HELIX 6 6 GLU A 301 GLN A 314 1 14 HELIX 7 7 GLU A 334 GLN A 338 5 5 HELIX 8 8 ASP A 339 ASN A 344 1 6 HELIX 9 9 ASP A 352 GLU A 358 5 7 SHEET 1 A 6 GLU A 323 PRO A 326 0 SHEET 2 A 6 SER A 292 TYR A 296 1 N SER A 292 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 252 N LEU A 203 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 SHEET 1 B 2 LYS A 281 GLN A 282 0 SHEET 2 B 2 ASP A 285 THR A 286 -1 O ASP A 285 N GLN A 282 SITE 1 AC1 7 HOH A 76 SER A 207 TRP A 209 TYR A 238 SITE 2 AC1 7 GLU A 250 ASP A 285 TYR A 290 CRYST1 43.933 50.305 66.556 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 0.022762 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015025 0.00000