HEADER OXIDOREDUCTASE 15-JAN-24 8XVO TITLE CRYSTAL STRUCTURE OF A SHORT-CHAIN DEHYDROGENASE/REDUCTASE 16 (SDR16) TITLE 2 FROM ANTRODIA CAMPHORATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHORT-CHAIN DEHYDROGENASE/REDUCTASE 16; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TAIWANOFUNGUS CAMPHORATUS; SOURCE 3 ORGANISM_TAXID: 2696576; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SHORT-CHAIN DEHYDROGENASE/REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.Q.ZHANG,M.ZHANG,M.YE REVDAT 1 15-JAN-25 8XVO 0 JRNL AUTH Y.Q.ZHANG,M.ZHANG,M.YE JRNL TITL CRYSTAL STRUCTURE OF A SHORT-CHAIN DEHYDROGENASE/REDUCTASE JRNL TITL 2 16 (SDR16) FROM ANTRODIA CAMPHORATA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.16_3549: ???) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23629 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1183 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 26.9000 - 3.8878 0.99 2938 157 0.1600 0.1600 REMARK 3 2 3.8878 - 3.0873 1.00 2840 149 0.1763 0.1959 REMARK 3 3 3.0873 - 2.6975 1.00 2820 133 0.2029 0.2540 REMARK 3 4 2.6975 - 2.4510 1.00 2798 142 0.1956 0.2383 REMARK 3 5 2.4510 - 2.2754 1.00 2791 142 0.1951 0.2280 REMARK 3 6 2.2754 - 2.1413 1.00 2754 156 0.1860 0.2566 REMARK 3 7 2.1413 - 2.0341 1.00 2758 152 0.1946 0.2313 REMARK 3 8 2.0341 - 1.9460 1.00 2747 152 0.2164 0.2576 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.350 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 : 0.007 2267 REMARK 3 ANGLE : 0.836 3076 REMARK 3 CHIRALITY : 0.051 356 REMARK 3 PLANARITY : 0.006 393 REMARK 3 DIHEDRAL : 22.213 834 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 8XVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-23 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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23687 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 51.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 5000 MME, 100MM MES/ REMARK 280 SODIUM HYDROXIDE PH 6.5, 200MM AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K 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 29.17950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.58450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.77400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.58450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.17950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.77400 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 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 ALA A 2 REMARK 465 HIS A 3 REMARK 465 TYR A 4 REMARK 465 SER A 5 REMARK 465 LEU A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 ALA A 10 REMARK 465 PRO A 11 REMARK 465 ARG A 12 REMARK 465 GLU A 303 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 THR A 39 30.03 -98.08 REMARK 500 ALA A 94 -144.89 -88.74 REMARK 500 HIS A 129 35.99 -142.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 8XVO A 1 303 PDB 8XVO 8XVO 1 303 SEQRES 1 A 303 MET ALA HIS TYR SER LEU SER SER SER ALA PRO ARG SER SEQRES 2 A 303 ARG SER ILE MET SER SER LEU SER ILE THR LEU ASN ASP SEQRES 3 A 303 GLY SER LYS ILE PRO TRP LEU GLY PHE GLY THR GLY THR SEQRES 4 A 303 ALA LEU TYR THR LYS ASP ALA GLU GLN ASP VAL LEU ARG SEQRES 5 A 303 ALA ILE ALA ASN GLY ILE VAL HIS LEU ASP GLY ALA GLN SEQRES 6 A 303 VAL TYR GLY ASN GLU ASP SER LEU GLY ALA ALA ILE ALA SEQRES 7 A 303 ALA SER GLY LYS PRO ARG GLN SER LEU TYR VAL THR THR SEQRES 8 A 303 LYS LEU ALA ALA VAL PRO ALA GLY GLN ASN VAL ARG ASP SEQRES 9 A 303 THR LEU VAL THR SER LEU LYS LYS LEU LYS LEU GLN TYR SEQRES 10 A 303 VAL ASP LEU PHE LEU ILE HIS THR PRO GLU GLN HIS GLN SEQRES 11 A 303 GLY ASN LEU LYS SER VAL TRP LYS GLN VAL GLU GLU LEU SEQRES 12 A 303 GLN LYS GLU GLY LEU ALA LYS SER ILE GLY VAL SER ASN SEQRES 13 A 303 PHE ARG VAL GLN ASP LEU GLU GLU ILE LEU ASP GLY ALA SEQRES 14 A 303 SER VAL VAL PRO ALA VAL ASN GLN ILE GLU TYR HIS PRO SEQRES 15 A 303 TYR VAL PHE LYS ALA ASP GLN PRO VAL ILE GLU TYR MET SEQRES 16 A 303 LYS LYS LYS ASN ILE VAL PRO THR SER TYR GLY GLY LEU SEQRES 17 A 303 THR PRO ILE VAL ARG PHE LYS GLY GLY PRO VAL ASP PRO SEQRES 18 A 303 VAL LEU ALA SER ILE ALA SER ARG VAL GLY THR THR ALA SEQRES 19 A 303 GLY GLN SER VAL SER GLU GLY GLN VAL LEU GLN LEU TRP SEQRES 20 A 303 LEU ARG ALA LYS GLY ILE PRO ALA ILE THR THR SER SER SEQRES 21 A 303 LYS GLU GLU ARG ILE LYS GLU TYR LEU ALA THR GLU THR SEQRES 22 A 303 LEU PRO GLY LEU THR PRO ALA GLU VAL GLN ALA ILE ASP SEQRES 23 A 303 GLU ALA GLY SER LYS ALA HIS HIS ARG VAL PHE SER LYS SEQRES 24 A 303 PHE TRP ASP GLU HET GOL A 401 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *147(H2 O) HELIX 1 AA1 TYR A 42 ASN A 56 1 15 HELIX 2 AA2 ASN A 69 GLY A 81 1 13 HELIX 3 AA3 PRO A 83 LEU A 87 5 5 HELIX 4 AA4 ASN A 101 LYS A 114 1 14 HELIX 5 AA5 THR A 125 HIS A 129 5 5 HELIX 6 AA6 ASN A 132 GLU A 146 1 15 HELIX 7 AA7 ARG A 158 ASP A 167 1 10 HELIX 8 AA8 HIS A 181 TYR A 183 5 3 HELIX 9 AA9 VAL A 184 ASN A 199 1 16 HELIX 10 AB1 LEU A 208 PHE A 214 1 7 HELIX 11 AB2 VAL A 219 GLY A 235 1 17 HELIX 12 AB3 SER A 239 GLY A 252 1 14 HELIX 13 AB4 LYS A 261 GLU A 272 1 12 HELIX 14 AB5 THR A 278 SER A 290 1 13 HELIX 15 AB6 SER A 298 ASP A 302 5 5 SHEET 1 AA1 2 SER A 21 THR A 23 0 SHEET 2 AA1 2 LYS A 29 PRO A 31 -1 O ILE A 30 N ILE A 22 SHEET 1 AA2 9 LEU A 33 GLY A 36 0 SHEET 2 AA2 9 HIS A 60 ASP A 62 1 O ASP A 62 N PHE A 35 SHEET 3 AA2 9 TYR A 88 LEU A 93 1 O TYR A 88 N LEU A 61 SHEET 4 AA2 9 VAL A 118 ILE A 123 1 O LEU A 122 N LEU A 93 SHEET 5 AA2 9 ALA A 149 SER A 155 1 O LYS A 150 N VAL A 118 SHEET 6 AA2 9 VAL A 175 GLU A 179 1 O VAL A 175 N VAL A 154 SHEET 7 AA2 9 VAL A 201 TYR A 205 1 O THR A 203 N ILE A 178 SHEET 8 AA2 9 ALA A 255 THR A 257 1 O ILE A 256 N SER A 204 SHEET 9 AA2 9 LEU A 33 GLY A 36 1 N GLY A 36 O THR A 257 CRYST1 58.359 69.548 77.169 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 0.017135 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012959 0.00000 CONECT 2221 2222 2223 CONECT 2222 2221 CONECT 2223 2221 2224 2225 CONECT 2224 2223 CONECT 2225 2223 2226 CONECT 2226 2225 MASTER 240 0 1 15 11 0 0 6 2372 1 6 24 END