HEADER PLANT PROTEIN 30-JAN-24 8Y4U TITLE CRYSTAL STRUCTURE OF A HIS1 FROM ORYZA SATIVA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FE(II)/2-OXOGLUTARATE-DEPENDENT OXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OS02G0280700 PROTEIN,CDNA CLONE:J013034J09,FULL INSERT COMPND 5 SEQUENCE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. JAPONICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: HIS1, LOC_OS02G17940, OS02G0280700, OSNPB_020280700; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HPPD INHIBITOR SENSITIVE 1; OXYGENASE;, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.WANG,J.M.MA,H.SHIBING,Y.BEIBEI,Z.HE,L.DANDAN REVDAT 2 03-APR-24 8Y4U 1 JRNL REVDAT 1 28-FEB-24 8Y4U 0 JRNL AUTH N.WANG,S.HE,B.YANG,H.ZHANG,D.LIU,P.SONG,T.CHEN,W.WANG,H.GE, JRNL AUTH 2 J.MA JRNL TITL CRYSTAL STRUCTURE OF HPPD INHIBITOR SENSITIVE PROTEIN FROM JRNL TITL 2 ORYZA SATIVA. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 704 49672 2024 JRNL REFN ESSN 1090-2104 JRNL PMID 38401306 JRNL DOI 10.1016/J.BBRC.2024.149672 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16981 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 865 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 19.5420 - 4.3477 1.00 2798 152 0.1849 0.1998 REMARK 3 2 4.3477 - 3.4572 1.00 2719 137 0.1804 0.2457 REMARK 3 3 3.4572 - 3.0220 1.00 2686 133 0.2095 0.2717 REMARK 3 4 3.0220 - 2.7465 1.00 2661 152 0.2226 0.2801 REMARK 3 5 2.7465 - 2.5501 1.00 2620 140 0.2410 0.2855 REMARK 3 6 2.5501 - 2.4000 1.00 2632 151 0.2460 0.3224 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.850 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 : 0.008 2379 REMARK 3 ANGLE : 0.885 3232 REMARK 3 CHIRALITY : 0.050 360 REMARK 3 PLANARITY : 0.006 427 REMARK 3 DIHEDRAL : 10.960 1429 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 46 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.7911 12.8952 31.3586 REMARK 3 T TENSOR REMARK 3 T11: 0.8845 T22: 0.6753 REMARK 3 T33: 0.3399 T12: -0.1910 REMARK 3 T13: 0.0246 T23: 0.0567 REMARK 3 L TENSOR REMARK 3 L11: 1.8241 L22: 1.1416 REMARK 3 L33: 3.0053 L12: -0.0917 REMARK 3 L13: 0.5335 L23: -0.6847 REMARK 3 S TENSOR REMARK 3 S11: -0.5122 S12: 1.0601 S13: -0.2605 REMARK 3 S21: -1.1844 S22: 0.4159 S23: -0.2555 REMARK 3 S31: 0.8029 S32: 0.0616 S33: 0.0934 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 84 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.7913 20.3349 60.3807 REMARK 3 T TENSOR REMARK 3 T11: 0.2600 T22: 0.3758 REMARK 3 T33: 0.3888 T12: -0.0387 REMARK 3 T13: -0.0112 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.8886 L22: 3.6018 REMARK 3 L33: 5.0084 L12: 0.4947 REMARK 3 L13: 0.1847 L23: -0.3479 REMARK 3 S TENSOR REMARK 3 S11: -0.0298 S12: -0.5672 S13: 0.2232 REMARK 3 S21: 0.2268 S22: -0.1417 S23: 0.2505 REMARK 3 S31: 0.0124 S32: -0.1980 S33: 0.1371 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.4795 15.2139 60.8227 REMARK 3 T TENSOR REMARK 3 T11: 0.2705 T22: 0.4596 REMARK 3 T33: 0.3288 T12: 0.0026 REMARK 3 T13: 0.0147 T23: 0.0526 REMARK 3 L TENSOR REMARK 3 L11: 3.4900 L22: 8.0726 REMARK 3 L33: 1.6995 L12: 2.0559 REMARK 3 L13: -0.6347 L23: 0.0983 REMARK 3 S TENSOR REMARK 3 S11: -0.0332 S12: -0.5416 S13: 0.2468 REMARK 3 S21: 0.0499 S22: 0.2188 S23: 1.0773 REMARK 3 S31: 0.1128 S32: -0.2299 S33: -0.1733 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 146 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.9098 26.9891 44.6322 REMARK 3 T TENSOR REMARK 3 T11: 0.4658 T22: 0.3510 REMARK 3 T33: 0.5557 T12: 0.0397 REMARK 3 T13: -0.1174 T23: 0.1160 REMARK 3 L TENSOR REMARK 3 L11: 2.5173 L22: 2.6253 REMARK 3 L33: 5.9214 L12: 1.8094 REMARK 3 L13: 0.5993 L23: -0.1843 REMARK 3 S TENSOR REMARK 3 S11: -0.6905 S12: 0.1351 S13: 0.9894 REMARK 3 S21: -0.5553 S22: 0.1296 S23: 0.7038 REMARK 3 S31: -0.9782 S32: -0.3464 S33: 0.4787 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 204 THROUGH 327 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.9064 10.9288 45.6991 REMARK 3 T TENSOR REMARK 3 T11: 0.3019 T22: 0.2946 REMARK 3 T33: 0.3248 T12: -0.0006 REMARK 3 T13: -0.0062 T23: 0.0594 REMARK 3 L TENSOR REMARK 3 L11: 2.2983 L22: 2.4909 REMARK 3 L33: 2.8316 L12: 1.0892 REMARK 3 L13: 1.2898 L23: -0.4352 REMARK 3 S TENSOR REMARK 3 S11: -0.2313 S12: 0.0474 S13: 0.2678 REMARK 3 S21: -0.3267 S22: 0.0794 S23: 0.2177 REMARK 3 S31: 0.0305 S32: -0.0335 S33: 0.1517 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 328 THROUGH 351 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.4983 13.8356 48.8349 REMARK 3 T TENSOR REMARK 3 T11: 0.4551 T22: 0.8520 REMARK 3 T33: 0.6558 T12: 0.0325 REMARK 3 T13: -0.1176 T23: -0.0618 REMARK 3 L TENSOR REMARK 3 L11: 8.8004 L22: 2.0994 REMARK 3 L33: 9.3750 L12: 2.9381 REMARK 3 L13: 2.0141 L23: 3.1188 REMARK 3 S TENSOR REMARK 3 S11: 0.1311 S12: -1.4753 S13: 0.4506 REMARK 3 S21: 0.2156 S22: 0.1863 S23: -0.5041 REMARK 3 S31: 0.3189 S32: -1.4900 S33: -0.3976 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 8Y4U 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_1300044845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16984 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.542 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 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: SAD 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 (%): 53.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES 25% PEG SMEAR MEDIUM, PH REMARK 280 6.5, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.21550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.51400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.20450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.21550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.51400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.20450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.21550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.51400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 65.20450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.21550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.51400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.20450 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: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 ASP A 3 REMARK 465 GLU A 4 REMARK 465 SER A 5 REMARK 465 TRP A 6 REMARK 465 ARG A 7 REMARK 465 ALA A 8 REMARK 465 PRO A 9 REMARK 465 ALA A 10 REMARK 465 ILE A 11 REMARK 465 VAL A 12 REMARK 465 GLN A 13 REMARK 465 GLU A 14 REMARK 465 LEU A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 ALA A 18 REMARK 465 GLY A 19 REMARK 465 VAL A 20 REMARK 465 GLU A 21 REMARK 465 GLU A 22 REMARK 465 PRO A 23 REMARK 465 PRO A 24 REMARK 465 SER A 25 REMARK 465 ARG A 26 REMARK 465 TYR A 27 REMARK 465 LEU A 28 REMARK 465 LEU A 29 REMARK 465 ARG A 30 REMARK 465 GLU A 31 REMARK 465 LYS A 32 REMARK 465 ASP A 33 REMARK 465 ARG A 34 REMARK 465 SER A 35 REMARK 465 ASP A 36 REMARK 465 VAL A 37 REMARK 465 LYS A 38 REMARK 465 LEU A 39 REMARK 465 VAL A 40 REMARK 465 ALA A 41 REMARK 465 ALA A 42 REMARK 465 GLU A 43 REMARK 465 LEU A 44 REMARK 465 PRO A 45 REMARK 465 GLY A 114 REMARK 465 LYS A 115 REMARK 465 VAL A 127 REMARK 465 VAL A 128 REMARK 465 ASP A 316 REMARK 465 LYS A 338 REMARK 465 PHE A 339 REMARK 465 SER A 340 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 ASP A 113 CG OD1 OD2 REMARK 470 GLN A 118 CG CD OE1 NE2 REMARK 470 ARG A 126 CG CD NE CZ NH1 NH2 REMARK 470 THR A 129 OG1 CG2 REMARK 470 GLU A 148 CG CD OE1 OE2 REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 GLU A 160 CG CD OE1 OE2 REMARK 470 LYS A 186 CG CD CE NZ REMARK 470 GLU A 192 CG CD OE1 OE2 REMARK 470 ASP A 193 CG OD1 OD2 REMARK 470 LEU A 196 CG CD1 CD2 REMARK 470 ARG A 198 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 305 CG CD OE1 OE2 REMARK 470 LYS A 306 CG CD CE NZ REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 ARG A 319 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 325 CG CD CE NZ REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 ARG A 341 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 343 CG CD OE1 OE2 REMARK 470 ILE A 351 CG1 CG2 CD1 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 ASP A 193 40.01 -103.16 REMARK 500 HIS A 260 33.56 72.47 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 FE A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 226 NE2 REMARK 620 2 ASP A 228 OD1 88.8 REMARK 620 3 HIS A 283 NE2 87.6 93.1 REMARK 620 4 HOH A 588 O 143.1 91.7 129.2 REMARK 620 N 1 2 3 DBREF 8Y4U A 1 351 UNP Q6ES21 Q6ES21_ORYSJ 1 351 SEQRES 1 A 351 MET ALA ASP GLU SER TRP ARG ALA PRO ALA ILE VAL GLN SEQRES 2 A 351 GLU LEU ALA ALA ALA GLY VAL GLU GLU PRO PRO SER ARG SEQRES 3 A 351 TYR LEU LEU ARG GLU LYS ASP ARG SER ASP VAL LYS LEU SEQRES 4 A 351 VAL ALA ALA GLU LEU PRO GLU PRO LEU PRO VAL VAL ASP SEQRES 5 A 351 LEU SER ARG LEU ASP GLY ALA GLU GLU ALA THR LYS LEU SEQRES 6 A 351 ARG VAL ALA LEU GLN ASN TRP GLY PHE PHE LEU LEU THR SEQRES 7 A 351 ASN HIS GLY VAL GLU ALA SER LEU MET ASP SER VAL MET SEQRES 8 A 351 ASN LEU SER ARG GLU PHE PHE ASN GLN PRO ILE GLU ARG SEQRES 9 A 351 LYS GLN LYS PHE SER ASN LEU ILE ASP GLY LYS ASN PHE SEQRES 10 A 351 GLN ILE GLN GLY TYR GLY THR ASP ARG VAL VAL THR GLN SEQRES 11 A 351 ASP GLN ILE LEU ASP TRP SER ASP ARG LEU HIS LEU ARG SEQRES 12 A 351 VAL GLU PRO LYS GLU GLU GLN ASP LEU ALA PHE TRP PRO SEQRES 13 A 351 ASP HIS PRO GLU SER PHE ARG ASP VAL LEU ASN LYS TYR SEQRES 14 A 351 ALA SER GLY THR LYS ARG ILE ARG ASP ASP ILE ILE GLN SEQRES 15 A 351 ALA MET ALA LYS LEU LEU GLU LEU ASP GLU ASP TYR PHE SEQRES 16 A 351 LEU ASP ARG LEU ASN GLU ALA PRO ALA PHE ALA ARG PHE SEQRES 17 A 351 ASN TYR TYR PRO PRO CYS PRO ARG PRO ASP LEU VAL PHE SEQRES 18 A 351 GLY ILE ARG PRO HIS SER ASP GLY THR LEU LEU THR ILE SEQRES 19 A 351 LEU LEU VAL ASP LYS ASP VAL SER GLY LEU GLN VAL GLN SEQRES 20 A 351 ARG ASP GLY LYS TRP SER ASN VAL GLU ALA THR PRO HIS SEQRES 21 A 351 THR LEU LEU ILE ASN LEU GLY ASP THR MET GLU VAL MET SEQRES 22 A 351 CYS ASN GLY ILE PHE ARG SER PRO VAL HIS ARG VAL VAL SEQRES 23 A 351 THR ASN ALA GLU LYS GLU ARG ILE SER LEU ALA MET LEU SEQRES 24 A 351 TYR SER VAL ASN ASP GLU LYS ASP ILE GLU PRO ALA ALA SEQRES 25 A 351 GLY LEU LEU ASP GLU ASN ARG PRO ALA ARG TYR ARG LYS SEQRES 26 A 351 VAL SER VAL GLU GLU PHE ARG ALA GLY ILE PHE GLY LYS SEQRES 27 A 351 PHE SER ARG GLY GLU ARG TYR ILE ASP SER LEU ARG ILE HET FE A 401 1 HETNAM FE FE (III) ION FORMUL 2 FE FE 3+ FORMUL 3 HOH *118(H2 O) HELIX 1 AA1 SER A 54 LEU A 56 5 3 HELIX 2 AA2 GLY A 58 TRP A 72 1 15 HELIX 3 AA3 GLU A 83 ASN A 99 1 17 HELIX 4 AA4 PRO A 101 LYS A 107 1 7 HELIX 5 AA5 GLN A 132 TRP A 136 5 5 HELIX 6 AA6 PRO A 146 GLN A 150 5 5 HELIX 7 AA7 ASP A 151 TRP A 155 5 5 HELIX 8 AA8 SER A 161 LEU A 188 1 28 HELIX 9 AA9 PHE A 195 ASN A 200 5 6 HELIX 10 AB1 GLY A 267 CYS A 274 1 8 HELIX 11 AB2 ALA A 311 LEU A 315 5 5 HELIX 12 AB3 SER A 327 GLY A 337 1 11 HELIX 13 AB4 ARG A 344 ARG A 350 5 7 SHEET 1 AA1 8 VAL A 50 ASP A 52 0 SHEET 2 AA1 8 PHE A 74 THR A 78 1 O LEU A 76 N VAL A 51 SHEET 3 AA1 8 LEU A 262 LEU A 266 -1 O LEU A 262 N LEU A 77 SHEET 4 AA1 8 LEU A 232 VAL A 237 -1 N LEU A 235 O LEU A 263 SHEET 5 AA1 8 ARG A 293 TYR A 300 -1 O MET A 298 N ILE A 234 SHEET 6 AA1 8 ALA A 204 TYR A 211 -1 N PHE A 205 O LEU A 299 SHEET 7 AA1 8 ASP A 138 GLU A 145 -1 N LEU A 142 O ALA A 206 SHEET 8 AA1 8 GLY A 121 TYR A 122 -1 N GLY A 121 O HIS A 141 SHEET 1 AA2 4 ILE A 223 HIS A 226 0 SHEET 2 AA2 4 HIS A 283 VAL A 285 -1 O HIS A 283 N HIS A 226 SHEET 3 AA2 4 LEU A 244 ARG A 248 -1 N GLN A 245 O ARG A 284 SHEET 4 AA2 4 LYS A 251 ASN A 254 -1 O LYS A 251 N ARG A 248 LINK NE2 HIS A 226 FE FE A 401 1555 1555 2.07 LINK OD1 ASP A 228 FE FE A 401 1555 1555 2.11 LINK NE2 HIS A 283 FE FE A 401 1555 1555 1.96 LINK FE FE A 401 O HOH A 588 1555 1555 2.72 CISPEP 1 GLU A 145 PRO A 146 0 0.31 CISPEP 2 HIS A 158 PRO A 159 0 -1.61 CISPEP 3 HIS A 158 PRO A 159 0 -0.68 CRYST1 64.431 101.028 130.409 90.00 90.00 90.00 I 2 2 2 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 0.015520 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009898 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007668 0.00000