HEADER OXIDOREDUCTASE 01-JUL-22 8DJX TITLE CYTOSOLIC ASCORBATE PEROXIDASE FROM SORGHUM BICOLOR - COMPOUND II COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-ASCORBATE PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.11; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SORGHUM BICOLOR; SOURCE 3 ORGANISM_COMMON: SORGHUM; SOURCE 4 ORGANISM_TAXID: 4558; SOURCE 5 GENE: SORBI_3001G410200; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOSOLIC ASCORBATE PEROXIDASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHANG,C.KANG REVDAT 3 25-OCT-23 8DJX 1 REMARK REVDAT 2 17-MAY-23 8DJX 1 JRNL REVDAT 1 18-JAN-23 8DJX 0 JRNL AUTH B.ZHANG,J.A.LEWIS,W.VERMERRIS,S.E.SATTLER,C.KANG JRNL TITL A SORGHUM ASCORBATE PEROXIDASE WITH FOUR BINDING SITES HAS JRNL TITL 2 ACTIVITY AGAINST ASCORBATE AND PHENYLPROPANOIDS. JRNL REF PLANT PHYSIOL. V. 192 102 2023 JRNL REFN ESSN 1532-2548 JRNL PMID 36575825 JRNL DOI 10.1093/PLPHYS/KIAC604 REMARK 2 REMARK 2 RESOLUTION. 1.34 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 49858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 41.4900 - 3.2400 0.99 3908 164 0.1538 0.1418 REMARK 3 2 3.2400 - 2.5700 1.00 3749 156 0.1404 0.1407 REMARK 3 3 2.5700 - 2.2400 1.00 3698 155 0.1236 0.1383 REMARK 3 4 2.2400 - 2.0400 1.00 3690 154 0.1209 0.1388 REMARK 3 5 2.0400 - 1.8900 1.00 3690 154 0.1286 0.1431 REMARK 3 6 1.8900 - 1.7800 1.00 3653 153 0.1244 0.1429 REMARK 3 7 1.7800 - 1.6900 1.00 3660 152 0.1267 0.1444 REMARK 3 8 1.6900 - 1.6200 1.00 3649 153 0.1297 0.1679 REMARK 3 9 1.6200 - 1.5600 1.00 3638 152 0.1322 0.1640 REMARK 3 10 1.5600 - 1.5000 0.99 3590 150 0.1442 0.1564 REMARK 3 11 1.5000 - 1.4600 0.98 3542 148 0.1514 0.1545 REMARK 3 12 1.4600 - 1.4100 0.91 3293 138 0.1681 0.2078 REMARK 3 13 1.4100 - 1.3800 0.78 2816 117 0.2124 0.2343 REMARK 3 14 1.3800 - 1.3400 0.35 1282 54 0.2857 0.3630 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.89 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8DJX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000265924. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49922 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 41.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 25.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.10 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: PHENIX REMARK 200 STARTING MODEL: 1OAG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LI2SO4, 0.1 M TRIS, PH 8.5 AND 30 REMARK 280 % PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 19.03500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.48600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.37100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.48600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.03500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.37100 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 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 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 661 O HOH A 675 1.92 REMARK 500 O HOH A 672 O HOH A 694 1.94 REMARK 500 O HOH A 714 O HOH A 761 2.00 REMARK 500 O HOH A 550 O HOH A 656 2.00 REMARK 500 O HOH A 669 O HOH A 778 2.01 REMARK 500 O HOH A 622 O HOH A 700 2.08 REMARK 500 O HOH A 682 O HOH A 710 2.09 REMARK 500 O HOH A 416 O HOH A 701 2.10 REMARK 500 OE2 GLU A 176 O HOH A 401 2.17 REMARK 500 O HOH A 641 O HOH A 740 2.18 REMARK 500 O HOH A 601 O HOH A 684 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 172 -81.68 -96.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 303 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 163 NE2 REMARK 620 2 HEM A 303 NA 92.3 REMARK 620 3 HEM A 303 NB 87.1 89.8 REMARK 620 4 HEM A 303 NC 87.3 179.0 89.3 REMARK 620 5 HEM A 303 ND 94.7 90.9 178.1 90.1 REMARK 620 6 HOH A 432 O 177.4 86.7 90.5 93.7 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 304 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 164 O REMARK 620 2 THR A 164 OG1 69.3 REMARK 620 3 THR A 180 OG1 65.7 102.6 REMARK 620 4 ASN A 182 O 96.1 163.4 77.2 REMARK 620 5 ASN A 182 OD1 137.1 131.9 72.6 64.3 REMARK 620 6 VAL A 185 O 89.8 92.8 143.2 78.8 120.1 REMARK 620 7 ASP A 187 OD1 125.4 57.4 133.7 134.2 90.8 82.6 REMARK 620 N 1 2 3 4 5 6 DBREF 8DJX A 1 250 UNP C5WNL8 C5WNL8_SORBI 1 250 SEQRES 1 A 250 MET ALA LYS SER TYR PRO THR VAL SER ALA GLU TYR SER SEQRES 2 A 250 GLU ALA VAL GLU LYS ALA ARG GLN LYS LEU ARG ALA LEU SEQRES 3 A 250 ILE ALA GLU LYS SER CYS ALA PRO LEU MET LEU ARG LEU SEQRES 4 A 250 ALA TRP HIS SER ALA GLY THR PHE ASP VAL SER SER ARG SEQRES 5 A 250 THR GLY GLY PRO PHE GLY THR MET LYS ASN PRO ALA GLU SEQRES 6 A 250 LEU ALA HIS GLY ALA ASN ALA GLY LEU ASP ILE ALA VAL SEQRES 7 A 250 ARG LEU LEU GLU PRO ILE LYS GLU GLU PHE PRO ILE LEU SEQRES 8 A 250 SER TYR ALA ASP PHE TYR GLN LEU ALA GLY VAL VAL ALA SEQRES 9 A 250 VAL GLU VAL THR GLY GLY PRO GLN ILE PRO PHE HIS PRO SEQRES 10 A 250 GLY ARG GLU ASP LYS PRO GLN PRO PRO PRO GLU GLY ARG SEQRES 11 A 250 LEU PRO ASP ALA THR LYS GLY SER ASP HIS LEU ARG GLN SEQRES 12 A 250 VAL PHE GLY LYS GLN MET GLY LEU SER ASP GLN ASP ILE SEQRES 13 A 250 VAL ALA LEU SER GLY GLY HIS THR LEU GLY ARG CYS HIS SEQRES 14 A 250 LYS GLU ARG SER GLY PHE GLU GLY ALA TRP THR SER ASN SEQRES 15 A 250 PRO LEU VAL PHE ASP ASN SER TYR PHE LYS GLU LEU LEU SEQRES 16 A 250 SER GLY ASP LYS GLU GLY LEU LEU GLN LEU PRO SER ASP SEQRES 17 A 250 LYS ALA LEU LEU SER ASP PRO ALA PHE ARG PRO LEU VAL SEQRES 18 A 250 ASP LYS TYR ALA ALA ASP GLU LYS ALA PHE PHE GLU ASP SEQRES 19 A 250 TYR LYS GLU ALA HIS LEU LYS LEU SER GLU LEU GLY PHE SEQRES 20 A 250 ALA ASP ALA HET SO4 A 301 5 HET SO4 A 302 5 HET HEM A 303 73 HET NA A 304 1 HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NA SODIUM ION HETSYN HEM HEME FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 NA NA 1+ FORMUL 6 HOH *384(H2 O) HELIX 1 AA1 SER A 9 LYS A 30 1 22 HELIX 2 AA2 CYS A 32 GLY A 45 1 14 HELIX 3 AA3 GLY A 58 LYS A 61 5 4 HELIX 4 AA4 ASN A 62 ALA A 67 1 6 HELIX 5 AA5 HIS A 68 ALA A 72 5 5 HELIX 6 AA6 GLY A 73 PHE A 88 1 16 HELIX 7 AA7 SER A 92 THR A 108 1 17 HELIX 8 AA8 GLY A 137 GLY A 146 1 10 HELIX 9 AA9 SER A 152 GLY A 161 1 10 HELIX 10 AB1 GLY A 162 LEU A 165 5 4 HELIX 11 AB2 ASN A 188 GLY A 197 1 10 HELIX 12 AB3 LEU A 205 ASP A 214 1 10 HELIX 13 AB4 ALA A 216 ASP A 227 1 12 HELIX 14 AB5 ASP A 227 GLU A 244 1 18 SHEET 1 AA1 2 ARG A 167 CYS A 168 0 SHEET 2 AA1 2 GLY A 177 ALA A 178 -1 O GLY A 177 N CYS A 168 LINK NE2 HIS A 163 FE HEM A 303 1555 1555 2.12 LINK O THR A 164 NA NA A 304 1555 1555 2.69 LINK OG1 THR A 164 NA NA A 304 1555 1555 3.14 LINK OG1 THR A 180 NA NA A 304 1555 1555 3.08 LINK O ASN A 182 NA NA A 304 1555 1555 2.83 LINK OD1 ASN A 182 NA NA A 304 1555 1555 2.90 LINK O VAL A 185 NA NA A 304 1555 1555 2.69 LINK OD1 ASP A 187 NA NA A 304 1555 1555 3.09 LINK FE HEM A 303 O HOH A 432 1555 1555 1.83 CRYST1 38.070 74.742 82.972 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 0.026267 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012052 0.00000