HEADER OXIDOREDUCTASE 05-AUG-26 44ND TITLE CRYSTAL STRUCTURE OF AN OXIDIZED FORM OF MOUSE MSRA COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL PEPTIDE METHIONINE SULFOXIDE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDE-METHIONINE (S)-S-OXIDE REDUCTASE,PEPTIDE MET(O) COMPND 5 REDUCTASE,PROTEIN-METHIONINE-S-OXIDE REDUCTASE,PMSR; COMPND 6 EC: 1.8.4.11; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MSRA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDIZED FORM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.M.SHIN,H.J.KIM HAWKES,S.H.PARK,H.S.KI,S.H.KIM,F.SHAH,G.DI TRAPANI, AUTHOR 2 K.F.TONISSEN,K.Y.HWANG REVDAT 1 28-OCT-26 44ND 0 JRNL AUTH B.SHIN,H.K.HAWKES,S.PARK,H.KI,S.KIM,F.SHAH,G.DI TRAPANI, JRNL AUTH 2 K.F.TONISSEN,K.Y.HWANG JRNL TITL STRUCTURAL BASIS FOR CYSTEINE-LINKED REDOX-STATE PLASTICITY JRNL TITL 2 IN MAMMALIAN METHIONINE SULFOXIDE REDUCTASE A. JRNL REF REDOX BIOL V. 97 04436 2026 JRNL REFN ESSN 2213-2317 JRNL PMID 42860110 JRNL DOI 10.1016/J.REDOX.2026.104436 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20_4459: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.600 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 15762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1580 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 4.1900 - 3.3300 1.00 1339 154 0.1476 0.1903 REMARK 3 2 3.3300 - 2.9100 1.00 1310 146 0.1801 0.2205 REMARK 3 3 2.9100 - 2.6400 1.00 1322 141 0.1857 0.1953 REMARK 3 4 2.6400 - 2.4500 1.00 1308 147 0.1729 0.2076 REMARK 3 5 2.4500 - 2.3100 1.00 1303 143 0.1702 0.2219 REMARK 3 6 2.3100 - 2.1900 1.00 1299 147 0.1525 0.2120 REMARK 3 7 2.1900 - 2.1000 1.00 1314 145 0.1493 0.2171 REMARK 3 8 2.1000 - 2.0200 1.00 1298 140 0.1536 0.2040 REMARK 3 9 2.0200 - 1.9500 1.00 1283 145 0.1498 0.1883 REMARK 3 10 1.9500 - 1.8900 0.79 1041 115 0.1601 0.2592 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1558 REMARK 3 ANGLE : 1.009 2106 REMARK 3 CHIRALITY : 0.057 212 REMARK 3 PLANARITY : 0.008 276 REMARK 3 DIHEDRAL : 6.396 210 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 44ND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-AUG-26. REMARK 100 THE DEPOSITION ID IS D_1300077918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15769 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, PH 9.0, 200 MM NACL, 26% REMARK 280 (W/V) PEG 3350, AND 4% (V/V) FORMAMIDE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.14133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.57067 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.35600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 5.78533 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.92667 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 MET A 1 REMARK 465 LEU A 2 REMARK 465 SER A 3 REMARK 465 ALA A 4 REMARK 465 SER A 5 REMARK 465 ARG A 6 REMARK 465 ARG A 7 REMARK 465 ALA A 8 REMARK 465 LEU A 9 REMARK 465 GLN A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 SER A 13 REMARK 465 SER A 14 REMARK 465 ALA A 15 REMARK 465 ASN A 16 REMARK 465 PRO A 17 REMARK 465 VAL A 18 REMARK 465 ARG A 19 REMARK 465 ARG A 20 REMARK 465 MET A 21 REMARK 465 GLY A 22 REMARK 465 ASP A 23 REMARK 465 SER A 24 REMARK 465 ALA A 25 REMARK 465 SER A 26 REMARK 465 LYS A 27 REMARK 465 VAL A 28 REMARK 465 ILE A 29 REMARK 465 SER A 30 REMARK 465 ALA A 31 REMARK 465 GLU A 32 REMARK 465 GLU A 33 REMARK 465 ALA A 34 REMARK 465 LEU A 35 REMARK 465 PRO A 36 REMARK 465 GLY A 37 REMARK 465 ARG A 38 REMARK 465 THR A 39 REMARK 465 GLU A 40 REMARK 465 PRO A 41 REMARK 465 ILE A 42 REMARK 465 PRO A 43 REMARK 465 VAL A 44 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 304 O HOH A 440 2.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 44ND A 1 233 UNP Q9D6Y7 MSRA_MOUSE 1 233 SEQADV 44ND SER A 234 UNP Q9D6Y7 EXPRESSION TAG SEQADV 44ND ALA A 235 UNP Q9D6Y7 EXPRESSION TAG SEQRES 1 A 235 MET LEU SER ALA SER ARG ARG ALA LEU GLN LEU LEU SER SEQRES 2 A 235 SER ALA ASN PRO VAL ARG ARG MET GLY ASP SER ALA SER SEQRES 3 A 235 LYS VAL ILE SER ALA GLU GLU ALA LEU PRO GLY ARG THR SEQRES 4 A 235 GLU PRO ILE PRO VAL THR ALA LYS HIS HIS VAL SER GLY SEQRES 5 A 235 ASN ARG THR VAL GLU PRO PHE PRO GLU GLY THR GLN MET SEQRES 6 A 235 ALA VAL PHE GLY MET GLY CYS PHE TRP GLY ALA GLU ARG SEQRES 7 A 235 LYS PHE TRP VAL LEU LYS GLY VAL TYR SER THR GLN VAL SEQRES 8 A 235 GLY PHE ALA GLY GLY HIS THR ARG ASN PRO THR TYR LYS SEQRES 9 A 235 GLU VAL CYS SER GLU LYS THR GLY HIS ALA GLU VAL VAL SEQRES 10 A 235 ARG VAL VAL TYR ARG PRO GLU HIS ILE SER PHE GLU GLU SEQRES 11 A 235 LEU LEU LYS VAL PHE TRP GLU ASN HIS ASP PRO THR GLN SEQRES 12 A 235 GLY MET ARG GLN GLY ASN ASP PHE GLY THR GLN TYR ARG SEQRES 13 A 235 SER ALA VAL TYR PRO THR SER ALA VAL GLN MET GLU ALA SEQRES 14 A 235 ALA LEU ARG SER LYS GLU GLU TYR GLN LYS VAL LEU SER SEQRES 15 A 235 LYS HIS ASN PHE GLY PRO ILE THR THR ASP ILE ARG GLU SEQRES 16 A 235 GLY GLN VAL PHE TYR TYR ALA GLU ASP TYR HIS GLN GLN SEQRES 17 A 235 TYR LEU SER LYS ASN PRO ASP GLY TYR CYS GLY LEU GLY SEQRES 18 A 235 GLY THR GLY VAL SER CYS PRO MET ALA ILE LYS LYS SER SEQRES 19 A 235 ALA FORMUL 2 HOH *177(H2 O) HELIX 1 AA1 CYS A 72 VAL A 82 1 11 HELIX 2 AA2 THR A 102 SER A 108 1 7 HELIX 3 AA3 SER A 127 ASN A 138 1 12 HELIX 4 AA4 THR A 153 TYR A 155 5 3 HELIX 5 AA5 SER A 163 HIS A 184 1 22 HELIX 6 AA6 GLU A 203 GLN A 207 5 5 HELIX 7 AA7 GLN A 208 ASN A 213 1 6 HELIX 8 AA8 SER A 226 ALA A 235 1 10 SHEET 1 AA1 6 ASP A 192 ILE A 193 0 SHEET 2 AA1 6 SER A 157 VAL A 159 1 N SER A 157 O ASP A 192 SHEET 3 AA1 6 GLN A 64 MET A 70 -1 N GLY A 69 O ALA A 158 SHEET 4 AA1 6 ALA A 114 TYR A 121 -1 O VAL A 119 N ALA A 66 SHEET 5 AA1 6 VAL A 86 ALA A 94 -1 N ALA A 94 O ALA A 114 SHEET 6 AA1 6 TYR A 200 TYR A 201 -1 O TYR A 200 N PHE A 93 SHEET 1 AA2 2 ARG A 146 GLN A 147 0 SHEET 2 AA2 2 ASP A 150 PHE A 151 -1 O ASP A 150 N GLN A 147 SSBOND 1 CYS A 72 CYS A 218 1555 1555 2.04 SSBOND 2 CYS A 107 CYS A 227 1555 1555 2.05 CISPEP 1 GLU A 57 PRO A 58 0 2.32 CRYST1 99.335 99.335 34.712 90.00 90.00 120.00 P 65 6 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 0.010067 0.005812 0.000000 0.00000 SCALE2 0.000000 0.011624 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028808 0.00000 CONECT 207 1408 CONECT 492 1458 CONECT 1408 207 CONECT 1458 492 MASTER 271 0 0 8 8 0 0 6 1692 1 4 19 END