HEADER OXIDOREDUCTASE 30-APR-26 26HF TITLE X-RAY CRYSTAL STRUCTURE OF THE APO-FORM OF DIFLAVIN-LINKED DISULFIDE TITLE 2 OXIDOREDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SLR0600 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIFLAVIN-LINKED DISULFIDE OXIDOREDUCTASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. PCC 6803; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 GENE: SLR0600; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FLAVOPROTEIN, CYANOBACTERIA, ELECTRON TRANSFER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.HIRANO,T.SUZUKI,N.UMEDA,Y.MINATO,K.YOSHIMURA,T.TAMADA,S.KIMURA REVDAT 1 28-OCT-26 26HF 0 JRNL AUTH Y.HIRANO,T.SUZUKI,N.UMEDA,Y.MINATO,K.YOSHIMURA,T.TAMADA, JRNL AUTH 2 S.KIMURA JRNL TITL CHARACTERIZATION OF FAD BINDING TO THE APO-FORM OF JRNL TITL 2 DIFLAVIN-LINKED DISULFIDE OXIDOREDUCTASE DERIVED FROM JRNL TITL 3 CYANOBACTERIUM SYNECHOCYSTIS SP. PCC6803. JRNL REF BIOCHEM.J. 2026 JRNL REFN ESSN 1470-8728 JRNL PMID 42821309 JRNL DOI 10.1042/BCJ20260320 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 6875 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.263 REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 332 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 46.9600 - 3.6600 1.00 3311 146 0.2215 0.2462 REMARK 3 2 3.6500 - 2.9000 0.99 3232 186 0.4012 0.3975 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) : 0.147 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 41.685 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 86.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 88.58 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 : 0.003 2540 REMARK 3 ANGLE : 0.633 3443 REMARK 3 CHIRALITY : 0.044 387 REMARK 3 PLANARITY : 0.006 437 REMARK 3 DIHEDRAL : 13.308 908 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 26HF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-APR-26. REMARK 100 THE DEPOSITION ID IS D_1300073647. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6924 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 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 : 1.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M POTASSIUM CHLORIDE, REMARK 280 50 MM TRIS-HCL PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 33.20750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 33.20750 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 71.77750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.20750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.88875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.20750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 107.66625 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.20750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.20750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 71.77750 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 33.20750 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 107.66625 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 33.20750 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 35.88875 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: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 66.41500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 VAL A 61 REMARK 465 GLY A 62 REMARK 465 LEU A 63 REMARK 465 ASP A 64 REMARK 465 PRO A 65 REMARK 465 ASP A 66 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 48 -134.16 60.94 REMARK 500 ASP A 56 96.90 -52.50 REMARK 500 ARG A 58 115.92 -175.12 REMARK 500 LYS A 111 -47.12 72.39 REMARK 500 TYR A 115 74.88 -117.35 REMARK 500 TYR A 148 -78.03 -117.66 REMARK 500 ASP A 163 18.55 57.97 REMARK 500 ALA A 205 -74.42 -59.34 REMARK 500 HIS A 227 -11.00 64.26 REMARK 500 ASN A 274 -151.31 -99.43 REMARK 500 PRO A 321 116.11 -31.79 REMARK 500 REMARK 500 REMARK: NULL DBREF 26HF A 1 326 UNP P74746 P74746_SYNY3 1 326 SEQRES 1 A 326 MET LYS LEU SER SER LYS ASN LEU ASP ALA ARG LEU ASP SEQRES 2 A 326 THR VAL TYR ASP ALA ILE VAL LEU GLY GLY GLY MET GLY SEQRES 3 A 326 GLY LEU SER ALA ALA ILE TYR LEU ALA ARG TYR GLY LEU SEQRES 4 A 326 LYS CYS LEU VAL VAL GLU LYS GLY ARG GLY ARG SER PHE SEQRES 5 A 326 TRP MET GLN ASP LEU ARG ASN TYR VAL GLY LEU ASP PRO SEQRES 6 A 326 ASP THR PRO GLY ARG ASP ILE ILE THR HIS SER THR GLN SEQRES 7 A 326 GLN ALA LEU HIS TRP GLY ALA ASP LEU LEU ARG GLY TYR SEQRES 8 A 326 VAL GLU ASP VAL THR ASP GLU GLY ASP THR LEU ALA VAL SEQRES 9 A 326 LYS VAL LYS VAL GLY LYS LYS ASP SER LEU TYR PRO ILE SEQRES 10 A 326 PHE ARG THR LYS TYR VAL ILE ALA ALA THR GLY ILE ILE SEQRES 11 A 326 ASP ASN LEU PRO GLN LEU GLU ASP MET GLN ASN VAL TYR SEQRES 12 A 326 ASP TYR ALA GLY TYR THR LEU HIS VAL CYS MET ILE CYS SEQRES 13 A 326 ASP GLY PHE ASP MET TRP ASP GLN LYS ALA VAL LEU ILE SEQRES 14 A 326 ALA GLY THR GLU GLY GLN ILE ASN ALA ALA PHE VAL LEU SEQRES 15 A 326 ASN TRP PHE THR PRO TYR ILE THR VAL LEU THR HIS GLY SEQRES 16 A 326 LEU CYS THR VAL GLY ASP GLU MET LYS ALA LYS LEU ALA SEQRES 17 A 326 ASP HIS GLY TYR PRO LEU HIS GLU ALA ALA ILE THR LYS SEQRES 18 A 326 PHE LEU GLY GLU ASP HIS LYS MET SER GLY VAL GLU LEU SEQRES 19 A 326 VAL ASP GLY THR VAL VAL GLU ALA THR THR GLY LEU ILE SEQRES 20 A 326 ASN MET GLY SER VAL TYR HIS ASN HIS TYR LEU LYS GLY SEQRES 21 A 326 ILE GLU GLY LEU GLU TRP ASP GLY GLU ASN LEU VAL THR SEQRES 22 A 326 ASN ASP MET ALA GLN THR SER HIS PRO ARG ILE PHE ALA SEQRES 23 A 326 LEU GLY ASP LEU LYS LYS GLY LEU ASN GLN VAL SER VAL SEQRES 24 A 326 ALA VAL ALA ASP GLY THR LEU ALA ALA THR GLN ILE TRP SEQRES 25 A 326 ARG ASN ILE ARG ARG ALA SER GLU PRO ARG LYS TRP ILE SEQRES 26 A 326 HIS HELIX 1 AA1 LYS A 6 ALA A 10 5 5 HELIX 2 AA2 GLY A 24 TYR A 37 1 14 HELIX 3 AA3 SER A 51 ASP A 56 1 6 HELIX 4 AA4 PRO A 68 GLY A 84 1 17 HELIX 5 AA5 MET A 139 ALA A 146 1 8 HELIX 6 AA6 CYS A 153 GLY A 158 1 6 HELIX 7 AA7 PHE A 159 TRP A 162 5 4 HELIX 8 AA8 GLY A 174 ASN A 177 5 4 HELIX 9 AA9 ALA A 178 ASN A 183 1 6 HELIX 10 AB1 GLY A 200 GLY A 211 1 12 HELIX 11 AB2 ASN A 255 LYS A 259 5 5 HELIX 12 AB3 GLY A 288 LYS A 291 5 4 HELIX 13 AB4 GLN A 296 ALA A 318 1 23 SHEET 1 AA1 4 VAL A 15 TYR A 16 0 SHEET 2 AA1 4 ILE A 117 THR A 120 1 O ARG A 119 N TYR A 16 SHEET 3 AA1 4 LEU A 102 LYS A 107 -1 N VAL A 104 O PHE A 118 SHEET 4 AA1 4 TYR A 91 ASP A 97 -1 N TYR A 91 O LYS A 107 SHEET 1 AA2 5 ASP A 86 ARG A 89 0 SHEET 2 AA2 5 CYS A 41 GLU A 45 1 N VAL A 43 O LEU A 88 SHEET 3 AA2 5 ALA A 18 LEU A 21 1 N VAL A 20 O LEU A 42 SHEET 4 AA2 5 VAL A 123 ALA A 125 1 O ILE A 124 N LEU A 21 SHEET 5 AA2 5 ILE A 284 ALA A 286 1 O PHE A 285 N ALA A 125 SHEET 1 AA3 2 ILE A 129 ASP A 131 0 SHEET 2 AA3 2 SER A 251 TYR A 253 -1 O VAL A 252 N ILE A 130 SHEET 1 AA4 5 LEU A 150 HIS A 151 0 SHEET 2 AA4 5 THR A 244 ASN A 248 1 O ILE A 247 N HIS A 151 SHEET 3 AA4 5 LYS A 165 ALA A 170 1 N VAL A 167 O LEU A 246 SHEET 4 AA4 5 TYR A 188 LEU A 192 1 O LEU A 192 N ALA A 170 SHEET 5 AA4 5 LEU A 214 HIS A 215 1 O HIS A 215 N VAL A 191 SHEET 1 AA5 3 ILE A 219 GLU A 225 0 SHEET 2 AA5 3 LYS A 228 LEU A 234 -1 O SER A 230 N LEU A 223 SHEET 3 AA5 3 VAL A 239 VAL A 240 -1 O VAL A 240 N VAL A 232 SHEET 1 AA6 2 TRP A 266 ASP A 267 0 SHEET 2 AA6 2 ASN A 270 LEU A 271 -1 O ASN A 270 N ASP A 267 SSBOND 1 CYS A 153 CYS A 156 1555 1555 2.04 CRYST1 66.415 66.415 143.555 90.00 90.00 90.00 I 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 0.015057 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006966 0.00000 CONECT 1149 1171 CONECT 1171 1149 MASTER 254 0 0 13 21 0 0 6 2489 1 2 26 END