HEADER BIOSYNTHETIC PROTEIN 05-APR-21 7EKD TITLE CRYSTAL STRUCTURE OF GIBBERELLIN 3-OXIDASE 2 (GA3OX2) IN RICE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GIBBERELLIN 3-BETA-DIOXYGENASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GA 3-OXIDASE 2,OSGA3OX2,GIBBERELLIN 3 BETA-HYDROXYLASE 2, COMPND 5 PROTEIN DWARF18; COMPND 6 EC: 1.14.11.15; COMPND 7 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: GA3OX2, D18, OS01G0177400, LOC_OS01G08220, OSJ_00594, SOURCE 6 P0013F10.29; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 2-OXOGLUTARATE-DEPENDENT DIOXYGENASE, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.TAKEHARA,K.KAWAI,B.MIKAMI,M.UEGUCHI-TANAKA REVDAT 2 29-NOV-23 7EKD 1 REMARK REVDAT 1 16-FEB-22 7EKD 0 JRNL AUTH K.KAWAI,S.TAKEHARA,T.KASHIO,M.MORII,A.SUGIHARA,H.YOSHIMURA, JRNL AUTH 2 A.ITO,M.HATTORI,Y.TODA,M.KOJIMA,Y.TAKEBAYASHI,H.FURUUMI, JRNL AUTH 3 K.I.NONOMURA,B.MIKAMI,T.AKAGI,H.SAKAKIBARA,H.KITANO, JRNL AUTH 4 M.MATSUOKA,M.UEGUCHI-TANAKA JRNL TITL EVOLUTIONARY ALTERATIONS IN GENE EXPRESSION AND ENZYMATIC JRNL TITL 2 ACTIVITIES OF GIBBERELLIN 3-OXIDASE 1 IN ORYZA. JRNL REF COMMUN BIOL V. 5 67 2022 JRNL REFN ESSN 2399-3642 JRNL PMID 35046494 JRNL DOI 10.1038/S42003-022-03008-5 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 27221 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) : 0.163 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1364 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 37.6900 - 4.0899 1.00 2671 146 0.1701 0.2091 REMARK 3 2 4.0899 - 3.2469 1.00 2639 121 0.1552 0.1616 REMARK 3 3 3.2469 - 2.8366 1.00 2573 140 0.1634 0.2226 REMARK 3 4 2.8366 - 2.5773 1.00 2601 148 0.1653 0.2187 REMARK 3 5 2.5773 - 2.3926 1.00 2576 149 0.1667 0.2148 REMARK 3 6 2.3926 - 2.2516 1.00 2589 143 0.1620 0.2584 REMARK 3 7 2.2516 - 2.1388 1.00 2586 130 0.1568 0.2284 REMARK 3 8 2.1388 - 2.0457 1.00 2610 121 0.1573 0.2453 REMARK 3 9 2.0457 - 1.9670 1.00 2552 129 0.1615 0.2117 REMARK 3 10 1.9670 - 1.8991 0.96 2460 137 0.1689 0.2516 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.75 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 : 0.021 2815 REMARK 3 ANGLE : 2.296 3839 REMARK 3 CHIRALITY : 0.151 401 REMARK 3 PLANARITY : 0.010 504 REMARK 3 DIHEDRAL : 13.821 1044 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 7EKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021606. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-15 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 : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27238 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.899 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6KU3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 HEPES (PH 7.0) AND 20% (W/V) PEG4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.79700 REMARK 290 SMTRY3 2 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: 350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 PRO A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 SER A 5 REMARK 465 HIS A 6 REMARK 465 LEU A 7 REMARK 465 LYS A 8 REMARK 465 ASN A 9 REMARK 465 PRO A 10 REMARK 465 LEU A 11 REMARK 465 ALA A 355 REMARK 465 ALA A 356 REMARK 465 ALA A 357 REMARK 465 ALA A 358 REMARK 465 ALA A 359 REMARK 465 ASP A 360 REMARK 465 GLU A 361 REMARK 465 HIS A 362 REMARK 465 ASP A 363 REMARK 465 ASP A 364 REMARK 465 VAL A 365 REMARK 465 ALA A 366 REMARK 465 ALA A 367 REMARK 465 ALA A 368 REMARK 465 ALA A 369 REMARK 465 ASP A 370 REMARK 465 VAL A 371 REMARK 465 HIS A 372 REMARK 465 ALA A 373 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 650 O HOH A 672 2.00 REMARK 500 O HOH A 638 O HOH A 729 2.05 REMARK 500 O HOH A 636 O HOH A 693 2.07 REMARK 500 O HOH A 515 O HOH A 719 2.11 REMARK 500 O HOH A 511 O HOH A 651 2.12 REMARK 500 O HOH A 789 O HOH A 798 2.13 REMARK 500 O HOH A 719 O HOH A 760 2.14 REMARK 500 O HOH A 805 O HOH A 807 2.15 REMARK 500 O HOH A 801 O HOH A 804 2.16 REMARK 500 O HOH A 661 O HOH A 785 2.17 REMARK 500 O4 PO4 A 403 O HOH A 501 2.17 REMARK 500 OE2 GLU A 88 O HOH A 502 2.17 REMARK 500 NH1 ARG A 85 O HOH A 503 2.18 REMARK 500 O HOH A 506 O HOH A 700 2.19 REMARK 500 O HOH A 735 O HOH A 774 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 574 O HOH A 751 1565 1.83 REMARK 500 O HOH A 622 O HOH A 658 1565 2.06 REMARK 500 O HOH A 681 O HOH A 710 2645 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 162 CB GLU A 162 CG -0.134 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 89 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 MET A 203 CG - SD - CE ANGL. DEV. = -13.3 DEGREES REMARK 500 ARG A 279 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 279 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES 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 SER A 150 -135.09 58.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 29 LEU A 30 -147.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue J5X A 407 DBREF 7EKD A 1 373 UNP Q9FU53 G3OX2_ORYSJ 1 373 SEQRES 1 A 373 MET PRO THR PRO SER HIS LEU LYS ASN PRO LEU CYS PHE SEQRES 2 A 373 ASP PHE ARG ALA ALA ARG ARG VAL PRO GLU THR HIS ALA SEQRES 3 A 373 TRP PRO GLY LEU ASP ASP HIS PRO VAL VAL ASP GLY GLY SEQRES 4 A 373 GLY GLY GLY GLY GLU ASP ALA VAL PRO VAL VAL ASP VAL SEQRES 5 A 373 GLY ALA GLY ASP ALA ALA ALA ARG VAL ALA ARG ALA ALA SEQRES 6 A 373 GLU GLN TRP GLY ALA PHE LEU LEU VAL GLY HIS GLY VAL SEQRES 7 A 373 PRO ALA ALA LEU LEU SER ARG VAL GLU GLU ARG VAL ALA SEQRES 8 A 373 ARG VAL PHE SER LEU PRO ALA SER GLU LYS MET ARG ALA SEQRES 9 A 373 VAL ARG GLY PRO GLY GLU PRO CYS GLY TYR GLY SER PRO SEQRES 10 A 373 PRO ILE SER SER PHE PHE SER LYS LEU MET TRP SER GLU SEQRES 11 A 373 GLY TYR THR PHE SER PRO SER SER LEU ARG SER GLU LEU SEQRES 12 A 373 ARG ARG LEU TRP PRO LYS SER GLY ASP ASP TYR LEU LEU SEQRES 13 A 373 PHE CYS ASP VAL MET GLU GLU PHE HIS LYS GLU MET ARG SEQRES 14 A 373 ARG LEU ALA ASP GLU LEU LEU ARG LEU PHE LEU ARG ALA SEQRES 15 A 373 LEU GLY LEU THR GLY GLU GLU VAL ALA GLY VAL GLU ALA SEQRES 16 A 373 GLU ARG ARG ILE GLY GLU ARG MET THR ALA THR VAL HIS SEQRES 17 A 373 LEU ASN TRP TYR PRO ARG CYS PRO GLU PRO ARG ARG ALA SEQRES 18 A 373 LEU GLY LEU ILE ALA HIS THR ASP SER GLY PHE PHE THR SEQRES 19 A 373 PHE VAL LEU GLN SER LEU VAL PRO GLY LEU GLN LEU PHE SEQRES 20 A 373 ARG ARG GLY PRO ASP ARG TRP VAL ALA VAL PRO ALA VAL SEQRES 21 A 373 ALA GLY ALA PHE VAL VAL ASN VAL GLY ASP LEU PHE HIS SEQRES 22 A 373 ILE LEU THR ASN GLY ARG PHE HIS SER VAL TYR HIS ARG SEQRES 23 A 373 ALA VAL VAL ASN ARG ASP ARG ASP ARG VAL SER LEU GLY SEQRES 24 A 373 TYR PHE LEU GLY PRO PRO PRO ASP ALA GLU VAL ALA PRO SEQRES 25 A 373 LEU PRO GLU ALA VAL PRO ALA GLY ARG SER PRO ALA TYR SEQRES 26 A 373 ARG ALA VAL THR TRP PRO GLU TYR MET ALA VAL ARG LYS SEQRES 27 A 373 LYS ALA PHE ALA THR GLY GLY SER ALA LEU LYS MET VAL SEQRES 28 A 373 SER THR ASP ALA ALA ALA ALA ALA ASP GLU HIS ASP ASP SEQRES 29 A 373 VAL ALA ALA ALA ALA ASP VAL HIS ALA HET PO4 A 401 5 HET PO4 A 402 5 HET PO4 A 403 5 HET PO4 A 404 5 HET AKG A 405 10 HET MPD A 406 8 HET J5X A 407 23 HETNAM PO4 PHOSPHATE ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM J5X GIBBERELLIN A9 FORMUL 2 PO4 4(O4 P 3-) FORMUL 6 AKG C5 H6 O5 FORMUL 7 MPD C6 H14 O2 FORMUL 8 J5X C19 H24 O4 FORMUL 9 HOH *307(H2 O) HELIX 1 AA1 PRO A 22 ALA A 26 5 5 HELIX 2 AA2 GLY A 42 ALA A 46 5 5 HELIX 3 AA3 ASP A 56 TRP A 68 1 13 HELIX 4 AA4 PRO A 79 LEU A 96 1 18 HELIX 5 AA5 PRO A 97 MET A 102 1 6 HELIX 6 AA6 ARG A 103 VAL A 105 5 3 HELIX 7 AA7 PRO A 117 PHE A 123 5 7 HELIX 8 AA8 SER A 135 SER A 137 5 3 HELIX 9 AA9 SER A 138 LEU A 143 1 6 HELIX 10 AB1 ARG A 144 LEU A 146 5 3 HELIX 11 AB2 GLY A 151 LEU A 183 1 33 HELIX 12 AB3 THR A 186 ARG A 198 1 13 HELIX 13 AB4 ARG A 198 MET A 203 1 6 HELIX 14 AB5 GLY A 269 THR A 276 1 8 HELIX 15 AB6 LEU A 313 VAL A 317 5 5 HELIX 16 AB7 THR A 329 GLY A 344 1 16 HELIX 17 AB8 SER A 346 SER A 352 1 7 SHEET 1 AA1 5 VAL A 35 ASP A 37 0 SHEET 2 AA1 5 ARG A 253 ALA A 256 1 O ALA A 256 N VAL A 36 SHEET 3 AA1 5 LEU A 244 ARG A 248 -1 N LEU A 246 O VAL A 255 SHEET 4 AA1 5 HIS A 285 ALA A 287 -1 O ARG A 286 N GLN A 245 SHEET 5 AA1 5 LEU A 224 HIS A 227 -1 N HIS A 227 O HIS A 285 SHEET 1 AA2 8 VAL A 49 ASP A 51 0 SHEET 2 AA2 8 ALA A 70 VAL A 74 1 O LEU A 72 N VAL A 50 SHEET 3 AA2 8 PHE A 264 VAL A 268 -1 O VAL A 266 N PHE A 71 SHEET 4 AA2 8 PHE A 233 GLN A 238 -1 N VAL A 236 O VAL A 265 SHEET 5 AA2 8 ARG A 295 GLY A 303 -1 O LEU A 302 N PHE A 233 SHEET 6 AA2 8 THR A 204 TYR A 212 -1 N TYR A 212 O ARG A 295 SHEET 7 AA2 8 GLU A 130 PHE A 134 -1 N TYR A 132 O LEU A 209 SHEET 8 AA2 8 GLY A 113 TYR A 114 -1 N GLY A 113 O THR A 133 CISPEP 1 GLY A 250 PRO A 251 0 3.41 SITE 1 AC1 6 HIS A 273 HIS A 281 HOH A 511 HOH A 519 SITE 2 AC1 6 HOH A 651 HOH A 664 SITE 1 AC2 6 HIS A 165 ARG A 169 THR A 204 ALA A 205 SITE 2 AC2 6 HOH A 557 HOH A 618 SITE 1 AC3 7 PHE A 247 ARG A 249 HIS A 281 HOH A 501 SITE 2 AC3 7 HOH A 541 HOH A 561 HOH A 631 SITE 1 AC4 3 ARG A 202 ALA A 308 GLU A 309 SITE 1 AC5 11 ASN A 210 TYR A 212 LEU A 224 HIS A 227 SITE 2 AC5 11 VAL A 236 LEU A 244 HIS A 285 ARG A 295 SITE 3 AC5 11 SER A 297 PHE A 301 J5X A 407 SITE 1 AC6 6 PRO A 118 PHE A 122 ARG A 337 LYS A 338 SITE 2 AC6 6 PHE A 341 J5X A 407 SITE 1 AC7 12 PRO A 117 PRO A 118 ILE A 119 THR A 206 SITE 2 AC7 12 ASP A 229 SER A 230 PHE A 301 MET A 334 SITE 3 AC7 12 ARG A 337 AKG A 405 MPD A 406 HOH A 645 CRYST1 56.838 45.594 68.538 90.00 102.26 90.00 P 1 21 1 2 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 0.017594 0.000000 0.003823 0.00000 SCALE2 0.000000 0.021933 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014931 0.00000