HEADER HYDROLASE 19-OCT-12 3W04 TITLE CRYSTAL STRUCTURE OF ORYZA SATIVA DWARF14 (D14) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DWARF 88 ESTERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 55-318; COMPND 5 SYNONYM: HYDROLASE, ALPHA/BETA FOLD FAMILY PROTEIN, EXPRESSED, COMPND 6 OS03G0203200 PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA JAPONICA GROUP; SOURCE 3 ORGANISM_COMMON: JAPANESE RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: D88, LOC_OS03G10620, OS03G0203200; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 STAR (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET47B KEYWDS STRIGOLACTONE SIGNALING, ALPHA/BETA HYDROLASE, STRIGOLACTONE KEYWDS 2 HYDROLYSIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KAGIYAMA,Y.HIRANO,T.MORI,S.Y.KIM,J.KYOZUKA,Y.SETO,S.YAMAGUCHI, AUTHOR 2 T.HAKOSHIMA REVDAT 3 27-MAR-13 3W04 1 REMARK REVDAT 2 06-FEB-13 3W04 1 JRNL REVDAT 1 23-JAN-13 3W04 0 JRNL AUTH M.KAGIYAMA,Y.HIRANO,T.MORI,S.Y.KIM,J.KYOZUKA,Y.SETO, JRNL AUTH 2 S.YAMAGUCHI,T.HAKOSHIMA JRNL TITL STRUCTURES OF D14 AND D14L IN THE STRIGOLACTONE AND KARRIKIN JRNL TITL 2 SIGNALING PATHWAYS JRNL REF GENES CELLS V. 18 147 2013 JRNL REFN ISSN 1356-9597 JRNL PMID 23301669 JRNL DOI 10.1111/GTC.12025 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 86870 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4583 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6305 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 321 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4073 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 452 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.062 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.067 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.006 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4362 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5956 ; 2.540 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 565 ; 5.806 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;28.186 ;22.135 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 680 ;13.230 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;18.593 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 684 ; 0.176 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3340 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2718 ; 1.466 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4403 ; 2.455 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1644 ; 3.522 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1545 ; 5.264 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3W04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-12. REMARK 100 THE RCSB ID CODE IS RCSB095717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : ROTATED-INCLINED DOUBLE-CRYSTAL REMARK 200 MONOCHROMATOR , SI (111) REMARK 200 OPTICS : MIRROS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91864 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61700 REMARK 200 FOR SHELL : 3.300 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: PDB ENTRY 1WOM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% PEG6000, 5% MPD, 0.1M NA-HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 23.99400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.61550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.09550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.61550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.99400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.09550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A 53 REMARK 465 PRO A 54 REMARK 465 GLY B 53 REMARK 465 ARG B 317 REMARK 465 TYR B 318 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 PRO B 54 CG CD 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 652 O HOH A 680 2.11 REMARK 500 O HOH A 557 O HOH A 684 2.15 REMARK 500 O HOH A 504 O HOH A 698 2.16 REMARK 500 NH2 ARG B 267 O1 EDO B 406 2.16 REMARK 500 OE2 GLU A 224 O HOH A 629 2.16 REMARK 500 O HOH A 652 O HOH A 701 2.17 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 TYR A 278 CZ TYR A 278 CE2 0.079 REMARK 500 VAL B 218 CB VAL B 218 CG1 -0.148 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 70 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASP A 115 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 118 CG - CD - NE ANGL. DEV. = -18.6 DEGREES REMARK 500 ASP A 123 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 128 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 134 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 159 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 159 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 160 NE - CZ - NH1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 162 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 LEU A 229 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 PHE A 230 CB - CG - CD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 PHE A 230 CB - CG - CD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP A 248 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 248 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP B 112 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG B 117 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 118 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP B 120 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 120 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ASP B 123 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP B 127 CB - CG - OD2 ANGL. DEV. = -8.4 DEGREES REMARK 500 ASP B 134 CB - CG - OD2 ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG B 137 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 159 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 TYR B 182 CD1 - CE1 - CZ ANGL. DEV. = -5.6 DEGREES REMARK 500 PHE B 230 CB - CG - CD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 PHE B 230 CB - CG - CD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG B 233 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP B 248 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG B 250 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 312 NE - CZ - NH2 ANGL. DEV. = -4.0 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 147 -127.02 59.89 REMARK 500 ARG A 175 123.72 -171.61 REMARK 500 ASN A 201 83.17 -162.46 REMARK 500 ALA A 303 54.44 -145.12 REMARK 500 ASP B 81 -167.13 -128.78 REMARK 500 SER B 147 -129.97 63.74 REMARK 500 ARG B 175 124.04 -171.20 REMARK 500 ASP B 179 78.91 -153.94 REMARK 500 SER B 180 -113.40 61.22 REMARK 500 ASN B 201 95.53 -160.87 REMARK 500 ALA B 303 51.92 -140.00 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 MPD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WO6 RELATED DB: PDB DBREF 3W04 A 55 318 UNP Q10QA5 Q10QA5_ORYSJ 55 318 DBREF 3W04 B 55 318 UNP Q10QA5 Q10QA5_ORYSJ 55 318 SEQADV 3W04 GLY A 53 UNP Q10QA5 EXPRESSION TAG SEQADV 3W04 PRO A 54 UNP Q10QA5 EXPRESSION TAG SEQADV 3W04 GLY B 53 UNP Q10QA5 EXPRESSION TAG SEQADV 3W04 PRO B 54 UNP Q10QA5 EXPRESSION TAG SEQRES 1 A 266 GLY PRO LYS LEU LEU GLN ILE LEU ASN VAL ARG VAL VAL SEQRES 2 A 266 GLY SER GLY GLU ARG VAL VAL VAL LEU SER HIS GLY PHE SEQRES 3 A 266 GLY THR ASP GLN SER ALA TRP SER ARG VAL LEU PRO TYR SEQRES 4 A 266 LEU THR ARG ASP HIS ARG VAL VAL LEU TYR ASP LEU VAL SEQRES 5 A 266 CYS ALA GLY SER VAL ASN PRO ASP HIS PHE ASP PHE ARG SEQRES 6 A 266 ARG TYR ASP ASN LEU ASP ALA TYR VAL ASP ASP LEU LEU SEQRES 7 A 266 ALA ILE LEU ASP ALA LEU ARG ILE PRO ARG CYS ALA PHE SEQRES 8 A 266 VAL GLY HIS SER VAL SER ALA MET ILE GLY ILE LEU ALA SEQRES 9 A 266 SER ILE ARG ARG PRO ASP LEU PHE ALA LYS LEU VAL LEU SEQRES 10 A 266 ILE GLY ALA SER PRO ARG PHE LEU ASN ASP SER ASP TYR SEQRES 11 A 266 HIS GLY GLY PHE GLU LEU GLU GLU ILE GLN GLN VAL PHE SEQRES 12 A 266 ASP ALA MET GLY ALA ASN TYR SER ALA TRP ALA THR GLY SEQRES 13 A 266 TYR ALA PRO LEU ALA VAL GLY ALA ASP VAL PRO ALA ALA SEQRES 14 A 266 VAL GLN GLU PHE SER ARG THR LEU PHE ASN MET ARG PRO SEQRES 15 A 266 ASP ILE SER LEU HIS VAL CYS GLN THR VAL PHE LYS THR SEQRES 16 A 266 ASP LEU ARG GLY VAL LEU GLY MET VAL ARG ALA PRO CYS SEQRES 17 A 266 VAL VAL VAL GLN THR THR ARG ASP VAL SER VAL PRO ALA SEQRES 18 A 266 SER VAL ALA ALA TYR LEU LYS ALA HIS LEU GLY GLY ARG SEQRES 19 A 266 THR THR VAL GLU PHE LEU GLN THR GLU GLY HIS LEU PRO SEQRES 20 A 266 HIS LEU SER ALA PRO SER LEU LEU ALA GLN VAL LEU ARG SEQRES 21 A 266 ARG ALA LEU ALA ARG TYR SEQRES 1 B 266 GLY PRO LYS LEU LEU GLN ILE LEU ASN VAL ARG VAL VAL SEQRES 2 B 266 GLY SER GLY GLU ARG VAL VAL VAL LEU SER HIS GLY PHE SEQRES 3 B 266 GLY THR ASP GLN SER ALA TRP SER ARG VAL LEU PRO TYR SEQRES 4 B 266 LEU THR ARG ASP HIS ARG VAL VAL LEU TYR ASP LEU VAL SEQRES 5 B 266 CYS ALA GLY SER VAL ASN PRO ASP HIS PHE ASP PHE ARG SEQRES 6 B 266 ARG TYR ASP ASN LEU ASP ALA TYR VAL ASP ASP LEU LEU SEQRES 7 B 266 ALA ILE LEU ASP ALA LEU ARG ILE PRO ARG CYS ALA PHE SEQRES 8 B 266 VAL GLY HIS SER VAL SER ALA MET ILE GLY ILE LEU ALA SEQRES 9 B 266 SER ILE ARG ARG PRO ASP LEU PHE ALA LYS LEU VAL LEU SEQRES 10 B 266 ILE GLY ALA SER PRO ARG PHE LEU ASN ASP SER ASP TYR SEQRES 11 B 266 HIS GLY GLY PHE GLU LEU GLU GLU ILE GLN GLN VAL PHE SEQRES 12 B 266 ASP ALA MET GLY ALA ASN TYR SER ALA TRP ALA THR GLY SEQRES 13 B 266 TYR ALA PRO LEU ALA VAL GLY ALA ASP VAL PRO ALA ALA SEQRES 14 B 266 VAL GLN GLU PHE SER ARG THR LEU PHE ASN MET ARG PRO SEQRES 15 B 266 ASP ILE SER LEU HIS VAL CYS GLN THR VAL PHE LYS THR SEQRES 16 B 266 ASP LEU ARG GLY VAL LEU GLY MET VAL ARG ALA PRO CYS SEQRES 17 B 266 VAL VAL VAL GLN THR THR ARG ASP VAL SER VAL PRO ALA SEQRES 18 B 266 SER VAL ALA ALA TYR LEU LYS ALA HIS LEU GLY GLY ARG SEQRES 19 B 266 THR THR VAL GLU PHE LEU GLN THR GLU GLY HIS LEU PRO SEQRES 20 B 266 HIS LEU SER ALA PRO SER LEU LEU ALA GLN VAL LEU ARG SEQRES 21 B 266 ARG ALA LEU ALA ARG TYR HET MPD A 401 8 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET EPE B 401 15 HET MPD B 402 8 HET EDO B 403 4 HET EDO B 404 4 HET EDO B 405 4 HET EDO B 406 4 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 3 MPD 2(C6 H14 O2) FORMUL 4 EDO 7(C2 H6 O2) FORMUL 7 EPE C8 H18 N2 O4 S FORMUL 13 HOH *452(H2 O) HELIX 1 1 LYS A 55 LEU A 60 1 6 HELIX 2 2 ASP A 81 SER A 86 5 6 HELIX 3 3 VAL A 88 LEU A 92 5 5 HELIX 4 4 ASN A 110 PHE A 114 5 5 HELIX 5 5 ARG A 117 ASP A 120 5 4 HELIX 6 6 ASN A 121 LEU A 136 1 16 HELIX 7 7 SER A 147 ARG A 160 1 14 HELIX 8 8 GLU A 187 ASN A 201 1 15 HELIX 9 9 ASN A 201 GLY A 215 1 15 HELIX 10 10 VAL A 218 ASN A 231 1 14 HELIX 11 11 ARG A 233 LYS A 246 1 14 HELIX 12 12 LEU A 249 VAL A 256 5 8 HELIX 13 13 ALA A 273 LEU A 283 1 11 HELIX 14 14 LEU A 298 ALA A 303 1 6 HELIX 15 15 ALA A 303 LEU A 315 1 13 HELIX 16 16 LYS B 55 LEU B 60 1 6 HELIX 17 17 ASP B 81 SER B 86 5 6 HELIX 18 18 VAL B 88 LEU B 92 5 5 HELIX 19 19 ASN B 110 PHE B 114 5 5 HELIX 20 20 ARG B 117 ASP B 120 5 4 HELIX 21 21 ASN B 121 LEU B 136 1 16 HELIX 22 22 SER B 147 ARG B 160 1 14 HELIX 23 23 GLU B 187 ASN B 201 1 15 HELIX 24 24 ASN B 201 GLY B 215 1 15 HELIX 25 25 VAL B 218 MET B 232 1 15 HELIX 26 26 ARG B 233 LYS B 246 1 14 HELIX 27 27 LEU B 249 VAL B 256 5 8 HELIX 28 28 SER B 274 LEU B 283 1 10 HELIX 29 29 LEU B 298 ALA B 303 1 6 HELIX 30 30 ALA B 303 ALA B 316 1 14 SHEET 1 A 7 ARG A 63 GLY A 66 0 SHEET 2 A 7 ARG A 97 LEU A 100 -1 O VAL A 98 N VAL A 65 SHEET 3 A 7 VAL A 71 SER A 75 1 N VAL A 72 O VAL A 99 SHEET 4 A 7 CYS A 141 HIS A 146 1 O VAL A 144 N VAL A 73 SHEET 5 A 7 PHE A 164 ILE A 170 1 O ALA A 165 N CYS A 141 SHEET 6 A 7 CYS A 260 GLN A 264 1 O VAL A 261 N LEU A 169 SHEET 7 A 7 THR A 287 PHE A 291 1 O GLU A 290 N VAL A 262 SHEET 1 B 7 ARG B 63 GLY B 66 0 SHEET 2 B 7 ARG B 97 LEU B 100 -1 O VAL B 98 N VAL B 65 SHEET 3 B 7 VAL B 71 SER B 75 1 N VAL B 72 O VAL B 99 SHEET 4 B 7 CYS B 141 HIS B 146 1 O VAL B 144 N SER B 75 SHEET 5 B 7 PHE B 164 ILE B 170 1 O VAL B 168 N GLY B 145 SHEET 6 B 7 CYS B 260 GLN B 264 1 O VAL B 261 N LEU B 169 SHEET 7 B 7 THR B 287 PHE B 291 1 O GLU B 290 N GLN B 264 SITE 1 AC1 5 TYR A 209 SER A 270 HOH A 652 HOH A 680 SITE 2 AC1 5 HOH A 701 SITE 1 AC2 4 TYR A 182 HIS A 183 SER A 274 VAL A 275 SITE 1 AC3 8 MET A 198 GLY A 199 ASN A 201 TYR A 202 SITE 2 AC3 8 PRO A 234 HOH A 512 PRO B 90 ARG B 312 SITE 1 AC4 4 ALA A 303 PRO A 304 SER A 305 LEU A 306 SITE 1 AC5 13 PHE A 230 ALA B 216 THR B 294 GLU B 295 SITE 2 AC5 13 SER B 302 ALA B 303 PRO B 304 SER B 305 SITE 3 AC5 13 LEU B 306 HOH B 646 HOH B 667 HOH B 703 SITE 4 AC5 13 HOH B 712 SITE 1 AC6 4 TYR B 209 SER B 270 HOH B 629 HOH B 658 SITE 1 AC7 6 ASP B 181 TYR B 182 HIS B 183 SER B 274 SITE 2 AC7 6 VAL B 275 HOH B 718 SITE 1 AC8 4 ASP B 120 HIS B 239 GLN B 242 THR B 243 SITE 1 AC9 5 GLN A 309 ARG A 312 ASP B 112 ARG B 233 SITE 2 AC9 5 HOH B 523 SITE 1 BC1 7 GLY B 185 ARG B 267 ASP B 268 VAL B 269 SITE 2 BC1 7 VAL B 271 PRO B 272 LYS B 280 CRYST1 47.988 88.191 121.231 90.00 90.00 90.00 P 21 21 21 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 0.020839 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008249 0.00000 MASTER 417 0 10 30 14 0 18 6 0 0 0 42 END