HEADER PLANT PROTEIN 17-AUG-17 6AP8 TITLE CRYSTAL STRUCTURE OF RICE D14 BOUND TO 2-(2-METHYL-3-NITROANILINO) TITLE 2 BENZOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: STRIGOLACTONE ESTERASE D14; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 52-318; COMPND 5 SYNONYM: PROTEIN DWARF 14,PROTEIN DWARF 88,PROTEIN HIGH-TILLERING COMPND 6 DWARF 2; COMPND 7 EC: 3.1.-.-; COMPND 8 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: D14, D88, HTD2, OS03G0203200, LOC_OS03G10620; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA GAMI 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST566 KEYWDS ALPHA/BETA HYDROLASE, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.HAMIAUX REVDAT 4 04-OCT-23 6AP8 1 REMARK REVDAT 3 09-MAY-18 6AP8 1 JRNL REVDAT 2 04-APR-18 6AP8 1 JRNL REVDAT 1 21-MAR-18 6AP8 0 JRNL AUTH C.HAMIAUX,R.S.M.DRUMMOND,Z.LUO,H.W.LEE,P.SHARMA,B.J.JANSSEN, JRNL AUTH 2 N.B.PERRY,W.A.DENNY,K.C.SNOWDEN JRNL TITL INHIBITION OF STRIGOLACTONE RECEPTORS BYN-PHENYLANTHRANILIC JRNL TITL 2 ACID DERIVATIVES: STRUCTURAL AND FUNCTIONAL INSIGHTS. JRNL REF J. BIOL. CHEM. V. 293 6530 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29523686 JRNL DOI 10.1074/JBC.RA117.001154 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.HAMIAUX,R.S.DRUMMOND,B.J.JANSSEN,S.E.LEDGER,J.M.COONEY, REMARK 1 AUTH 2 R.D.NEWCOMB,K.C.SNOWDEN REMARK 1 TITL DAD2 IS AN ALPHA/BETA HYDROLASE LIKELY TO BE INVOLVED IN THE REMARK 1 TITL 2 PERCEPTION OF THE PLANT BRANCHING HORMONE, STRIGOLACTONE. REMARK 1 REF CURR. BIOL. V. 22 2032 2012 REMARK 1 REFN ISSN 1879-0445 REMARK 1 PMID 22959345 REMARK 1 DOI 10.1016/J.CUB.2012.08.007 REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 127214 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) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 6862 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) : 1.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9294 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 488 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4116 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 647 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.35000 REMARK 3 B22 (A**2) : 0.68000 REMARK 3 B33 (A**2) : 0.67000 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): 0.038 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.573 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4508 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4334 ; 0.012 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6186 ; 1.958 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9907 ; 1.763 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 598 ; 6.016 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;26.064 ;21.872 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 702 ;11.348 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;17.387 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 704 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5273 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1147 ; 0.014 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 8842 ; 3.331 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 139 ;30.654 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 9221 ;11.080 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 53 317 B 53 317 31812 0.130 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6AP8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000229531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-15 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 134179 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 REMARK 200 RESOLUTION RANGE LOW (A) : 48.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.30 REMARK 200 R MERGE FOR SHELL (I) : 1.99200 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: PHASER 2.5.7 REMARK 200 STARTING MODEL: 3W04 REMARK 200 REMARK 200 REMARK: ROD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES 0.1M, MPD 5%, PEG 6000 8%, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 24.00250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.51300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.21650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.51300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.00250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.21650 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 300 REMARK: MONOMER AS DETERMINED BY GEL FILTRATION 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 50 REMARK 465 GLY A 51 REMARK 465 SER A 52 REMARK 465 GLY B 50 REMARK 465 GLY B 51 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 B 579 O HOH B 733 1.94 REMARK 500 O2 BNY A 401 O HOH A 501 1.97 REMARK 500 OG1 THR A 294 O HOH A 502 1.99 REMARK 500 NH2 ARG B 70 O LEU B 315 2.04 REMARK 500 O HOH A 723 O HOH B 711 2.05 REMARK 500 NH1 ARG B 118 O HOH B 501 2.13 REMARK 500 ND2 ASN B 121 O HOH B 502 2.15 REMARK 500 O HOH B 724 O HOH B 799 2.16 REMARK 500 O HOH A 507 O HOH A 711 2.17 REMARK 500 OD1 ASN B 231 O HOH B 503 2.17 REMARK 500 OD2 ASP B 95 NH2 ARG B 312 2.17 REMARK 500 O HOH A 581 O HOH A 763 2.18 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 776 O HOH B 530 2454 1.99 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 GLY A 53 N GLY A 53 CA 0.099 REMARK 500 SER A 147 CA SER A 147 CB 0.125 REMARK 500 SER A 147 CB SER A 147 OG -0.109 REMARK 500 GLN A 193 CD GLN A 193 NE2 -0.157 REMARK 500 TYR A 318 CE1 TYR A 318 CZ -0.081 REMARK 500 SER B 147 CA SER B 147 CB 0.158 REMARK 500 SER B 147 CB SER B 147 OG -0.163 REMARK 500 GLU B 189 CD GLU B 189 OE1 0.079 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 ASP A 95 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP A 123 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 159 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 GLU A 187 OE1 - CD - OE2 ANGL. DEV. = -8.3 DEGREES REMARK 500 PHE A 230 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 233 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 CYS A 260 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 267 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 286 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 313 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 313 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG B 70 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 87 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP B 123 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 SER B 147 N - CA - CB ANGL. DEV. = -9.3 DEGREES REMARK 500 ARG B 250 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 267 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 267 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 313 NE - CZ - NH1 ANGL. DEV. = 3.5 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 -127.23 61.76 REMARK 500 ARG A 175 120.26 -171.18 REMARK 500 ASN A 201 79.04 -159.94 REMARK 500 GLN A 293 36.56 -96.46 REMARK 500 GLN A 293 42.56 -96.46 REMARK 500 ALA A 303 54.38 -146.56 REMARK 500 ASP B 81 -167.27 -119.74 REMARK 500 SER B 147 -124.74 60.94 REMARK 500 ARG B 175 119.50 -173.70 REMARK 500 ASP B 181 17.99 56.63 REMARK 500 ASN B 201 79.45 -157.18 REMARK 500 ALA B 303 53.43 -144.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 837 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 838 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH B 808 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH B 809 DISTANCE = 6.67 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BNY A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BNY B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W04 RELATED DB: PDB REMARK 900 3W04 IS THE APO STRUCTURE DBREF 6AP8 A 52 318 UNP Q10QA5 D14_ORYSJ 52 318 DBREF 6AP8 B 52 318 UNP Q10QA5 D14_ORYSJ 52 318 SEQADV 6AP8 GLY A 50 UNP Q10QA5 EXPRESSION TAG SEQADV 6AP8 GLY A 51 UNP Q10QA5 EXPRESSION TAG SEQADV 6AP8 GLY B 50 UNP Q10QA5 EXPRESSION TAG SEQADV 6AP8 GLY B 51 UNP Q10QA5 EXPRESSION TAG SEQRES 1 A 269 GLY GLY SER GLY ALA LYS LEU LEU GLN ILE LEU ASN VAL SEQRES 2 A 269 ARG VAL VAL GLY SER GLY GLU ARG VAL VAL VAL LEU SER SEQRES 3 A 269 HIS GLY PHE GLY THR ASP GLN SER ALA TRP SER ARG VAL SEQRES 4 A 269 LEU PRO TYR LEU THR ARG ASP HIS ARG VAL VAL LEU TYR SEQRES 5 A 269 ASP LEU VAL CYS ALA GLY SER VAL ASN PRO ASP HIS PHE SEQRES 6 A 269 ASP PHE ARG ARG TYR ASP ASN LEU ASP ALA TYR VAL ASP SEQRES 7 A 269 ASP LEU LEU ALA ILE LEU ASP ALA LEU ARG ILE PRO ARG SEQRES 8 A 269 CYS ALA PHE VAL GLY HIS SER VAL SER ALA MET ILE GLY SEQRES 9 A 269 ILE LEU ALA SER ILE ARG ARG PRO ASP LEU PHE ALA LYS SEQRES 10 A 269 LEU VAL LEU ILE GLY ALA SER PRO ARG PHE LEU ASN ASP SEQRES 11 A 269 SER ASP TYR HIS GLY GLY PHE GLU LEU GLU GLU ILE GLN SEQRES 12 A 269 GLN VAL PHE ASP ALA MET GLY ALA ASN TYR SER ALA TRP SEQRES 13 A 269 ALA THR GLY TYR ALA PRO LEU ALA VAL GLY ALA ASP VAL SEQRES 14 A 269 PRO ALA ALA VAL GLN GLU PHE SER ARG THR LEU PHE ASN SEQRES 15 A 269 MET ARG PRO ASP ILE SER LEU HIS VAL CYS GLN THR VAL SEQRES 16 A 269 PHE LYS THR ASP LEU ARG GLY VAL LEU GLY MET VAL ARG SEQRES 17 A 269 ALA PRO CYS VAL VAL VAL GLN THR THR ARG ASP VAL SER SEQRES 18 A 269 VAL PRO ALA SER VAL ALA ALA TYR LEU LYS ALA HIS LEU SEQRES 19 A 269 GLY GLY ARG THR THR VAL GLU PHE LEU GLN THR GLU GLY SEQRES 20 A 269 HIS LEU PRO HIS LEU SER ALA PRO SER LEU LEU ALA GLN SEQRES 21 A 269 VAL LEU ARG ARG ALA LEU ALA ARG TYR SEQRES 1 B 269 GLY GLY SER GLY ALA LYS LEU LEU GLN ILE LEU ASN VAL SEQRES 2 B 269 ARG VAL VAL GLY SER GLY GLU ARG VAL VAL VAL LEU SER SEQRES 3 B 269 HIS GLY PHE GLY THR ASP GLN SER ALA TRP SER ARG VAL SEQRES 4 B 269 LEU PRO TYR LEU THR ARG ASP HIS ARG VAL VAL LEU TYR SEQRES 5 B 269 ASP LEU VAL CYS ALA GLY SER VAL ASN PRO ASP HIS PHE SEQRES 6 B 269 ASP PHE ARG ARG TYR ASP ASN LEU ASP ALA TYR VAL ASP SEQRES 7 B 269 ASP LEU LEU ALA ILE LEU ASP ALA LEU ARG ILE PRO ARG SEQRES 8 B 269 CYS ALA PHE VAL GLY HIS SER VAL SER ALA MET ILE GLY SEQRES 9 B 269 ILE LEU ALA SER ILE ARG ARG PRO ASP LEU PHE ALA LYS SEQRES 10 B 269 LEU VAL LEU ILE GLY ALA SER PRO ARG PHE LEU ASN ASP SEQRES 11 B 269 SER ASP TYR HIS GLY GLY PHE GLU LEU GLU GLU ILE GLN SEQRES 12 B 269 GLN VAL PHE ASP ALA MET GLY ALA ASN TYR SER ALA TRP SEQRES 13 B 269 ALA THR GLY TYR ALA PRO LEU ALA VAL GLY ALA ASP VAL SEQRES 14 B 269 PRO ALA ALA VAL GLN GLU PHE SER ARG THR LEU PHE ASN SEQRES 15 B 269 MET ARG PRO ASP ILE SER LEU HIS VAL CYS GLN THR VAL SEQRES 16 B 269 PHE LYS THR ASP LEU ARG GLY VAL LEU GLY MET VAL ARG SEQRES 17 B 269 ALA PRO CYS VAL VAL VAL GLN THR THR ARG ASP VAL SER SEQRES 18 B 269 VAL PRO ALA SER VAL ALA ALA TYR LEU LYS ALA HIS LEU SEQRES 19 B 269 GLY GLY ARG THR THR VAL GLU PHE LEU GLN THR GLU GLY SEQRES 20 B 269 HIS LEU PRO HIS LEU SER ALA PRO SER LEU LEU ALA GLN SEQRES 21 B 269 VAL LEU ARG ARG ALA LEU ALA ARG TYR HET BNY A 401 20 HET GOL A 402 6 HET BNY B 401 20 HET GOL B 402 6 HETNAM BNY 2-[(2-METHYL-3-NITROPHENYL)AMINO]BENZOIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 BNY 2(C14 H12 N2 O4) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *647(H2 O) HELIX 1 AA1 GLY A 53 LEU A 60 1 8 HELIX 2 AA2 ASP A 81 SER A 86 5 6 HELIX 3 AA3 VAL A 88 LEU A 92 5 5 HELIX 4 AA4 ASN A 110 PHE A 114 5 5 HELIX 5 AA5 ARG A 117 ASP A 120 5 4 HELIX 6 AA6 ASN A 121 LEU A 136 1 16 HELIX 7 AA7 SER A 147 ARG A 160 1 14 HELIX 8 AA8 GLU A 187 ASN A 201 1 15 HELIX 9 AA9 ASN A 201 GLY A 215 1 15 HELIX 10 AB1 VAL A 218 MET A 232 1 15 HELIX 11 AB2 ARG A 233 LYS A 246 1 14 HELIX 12 AB3 LEU A 249 VAL A 256 5 8 HELIX 13 AB4 PRO A 272 LEU A 283 1 12 HELIX 14 AB5 LEU A 298 ALA A 303 1 6 HELIX 15 AB6 ALA A 303 LEU A 315 1 13 HELIX 16 AB7 GLY B 53 LEU B 60 1 8 HELIX 17 AB8 ASP B 81 SER B 86 5 6 HELIX 18 AB9 VAL B 88 LEU B 92 5 5 HELIX 19 AC1 ASN B 110 PHE B 114 5 5 HELIX 20 AC2 ARG B 117 ASP B 120 5 4 HELIX 21 AC3 ASN B 121 LEU B 136 1 16 HELIX 22 AC4 SER B 147 ARG B 160 1 14 HELIX 23 AC5 GLU B 187 ASN B 201 1 15 HELIX 24 AC6 ASN B 201 GLY B 215 1 15 HELIX 25 AC7 VAL B 218 MET B 232 1 15 HELIX 26 AC8 ARG B 233 LYS B 246 1 14 HELIX 27 AC9 LEU B 249 VAL B 256 5 8 HELIX 28 AD1 PRO B 272 LEU B 283 1 12 HELIX 29 AD2 LEU B 298 ALA B 303 1 6 HELIX 30 AD3 ALA B 303 ALA B 316 1 14 SHEET 1 AA1 7 ARG A 63 GLY A 66 0 SHEET 2 AA1 7 ARG A 97 LEU A 100 -1 O VAL A 98 N VAL A 65 SHEET 3 AA1 7 VAL A 71 SER A 75 1 N VAL A 72 O VAL A 99 SHEET 4 AA1 7 CYS A 141 HIS A 146 1 O VAL A 144 N VAL A 73 SHEET 5 AA1 7 PHE A 164 ILE A 170 1 O ALA A 165 N CYS A 141 SHEET 6 AA1 7 CYS A 260 GLN A 264 1 O VAL A 263 N LEU A 169 SHEET 7 AA1 7 THR A 287 PHE A 291 1 O THR A 288 N VAL A 262 SHEET 1 AA2 7 ARG B 63 GLY B 66 0 SHEET 2 AA2 7 ARG B 97 LEU B 100 -1 O VAL B 98 N VAL B 65 SHEET 3 AA2 7 VAL B 71 SER B 75 1 N LEU B 74 O VAL B 99 SHEET 4 AA2 7 CYS B 141 HIS B 146 1 O VAL B 144 N VAL B 73 SHEET 5 AA2 7 PHE B 164 ILE B 170 1 O VAL B 168 N PHE B 143 SHEET 6 AA2 7 CYS B 260 THR B 265 1 O VAL B 263 N LEU B 169 SHEET 7 AA2 7 THR B 287 LEU B 292 1 O GLU B 290 N VAL B 262 SITE 1 AC1 11 PHE A 78 SER A 147 PHE A 176 PHE A 186 SITE 2 AC1 11 VAL A 194 TRP A 205 CYS A 241 SER A 270 SITE 3 AC1 11 HIS A 297 HOH A 501 HOH A 568 SITE 1 AC2 5 TYR A 182 HIS A 183 SER A 274 VAL A 275 SITE 2 AC2 5 HOH A 538 SITE 1 AC3 13 PHE B 78 SER B 147 PHE B 176 PHE B 186 SITE 2 AC3 13 VAL B 194 CYS B 241 VAL B 244 PHE B 245 SITE 3 AC3 13 SER B 270 HIS B 297 HOH B 544 HOH B 570 SITE 4 AC3 13 HOH B 669 SITE 1 AC4 8 ASP B 181 TYR B 182 HIS B 183 GLY B 208 SITE 2 AC4 8 PRO B 211 LEU B 212 SER B 274 VAL B 275 CRYST1 48.005 88.433 119.026 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 0.020831 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008402 0.00000