HEADER HYDROLASE 17-MAR-09 3GNO
TITLE CRYSTAL STRUCTURE OF A RICE OS3BGLU6 BETA-GLUCOSIDASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: OS03G0212800 PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 38-521;
COMPND 5 SYNONYM: BETA-GLUCOSIDASE, GLYCOSYL HYDROLASE FAMILY 1 PROTEIN,
COMPND 6 EXPRESSED;
COMPND 7 EC: 3.2.1.21;
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: LOC_OS03G11420, OS03G0212800, OS3BGLU6 LOCUS ID: OS03G0212800;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32A+/DEST
KEYWDS BETA-ALPHA BARREL, GLYCOSIDASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.SESHADRI,T.AKIYAMA,R.OPASSIRI,B.KUAPRASERT,J.R.K.CAIRNS
REVDAT 4 06-NOV-24 3GNO 1 REMARK
REVDAT 3 01-NOV-23 3GNO 1 REMARK SEQADV
REVDAT 2 13-JUL-11 3GNO 1 VERSN
REVDAT 1 21-JUL-09 3GNO 0
JRNL AUTH S.SESHADRI,T.AKIYAMA,R.OPASSIRI,B.KUAPRASERT,J.R.K.CAIRNS
JRNL TITL STRUCTURAL AND ENZYMATIC CHARACTERIZATION OF OS3BGLU6, A
JRNL TITL 2 RICE {BETA}-GLUCOSIDASE HYDROLYZING HYDROPHOBIC GLYCOSIDES
JRNL TITL 3 AND (1->3)- AND (1->2)-LINKED DISACCHARIDES.
JRNL REF PLANT PHYSIOL. 2009
JRNL REFN ESSN 1532-2548
JRNL PMID 19587102
JRNL DOI 10.1104/PP.109.139436
REMARK 2
REMARK 2 RESOLUTION. 1.83 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.80
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 44199
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) : 0.166
REMARK 3 R VALUE (WORKING SET) : 0.164
REMARK 3 FREE R VALUE : 0.204
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2347
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) : 1.83
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88
REMARK 3 REFLECTION IN BIN (WORKING SET) : 3216
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.86
REMARK 3 BIN R VALUE (WORKING SET) : 0.1920
REMARK 3 BIN FREE R VALUE SET COUNT : 156
REMARK 3 BIN FREE R VALUE : 0.2760
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3836
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 44
REMARK 3 SOLVENT ATOMS : 466
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 14.89
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.44
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.01000
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): 0.124
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.399
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4019 ; 0.013 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5455 ; 1.321 ; 1.932
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 484 ;12.806 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;33.867 ;23.498
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 617 ;12.858 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;19.420 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 560 ; 0.097 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3132 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2001 ; 0.203 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2741 ; 0.314 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 428 ; 0.135 ; 0.200
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): 37 ; 0.228 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.172 ; 0.200
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): 2390 ; 0.702 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3833 ; 1.254 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1629 ; 2.070 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1618 ; 3.134 ; 4.500
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): 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 : 1.20
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 3GNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-09.
REMARK 100 THE DEPOSITION ID IS D_1000052087.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-AUG-08
REMARK 200 TEMPERATURE (KELVIN) : 110
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSRRC
REMARK 200 BEAMLINE : BL13B1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45193
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9
REMARK 200 DATA REDUNDANCY : 7.000
REMARK 200 R MERGE (I) : 0.09500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9900
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8
REMARK 200 DATA REDUNDANCY IN SHELL : 6.90
REMARK 200 R MERGE FOR SHELL (I) : 0.36600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900
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 1CBG
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.95
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 5000 MME, 0.1M BIS-TRIS, PH
REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K
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 28.40450
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.85500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.24450
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.85500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.40450
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.24450
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 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 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 SER A 1
REMARK 465 PHE A 2
REMARK 465 THR A 3
REMARK 465 MET A 4
REMARK 465 ALA A 5
REMARK 465 GLN A 6
REMARK 465 GLN A 7
REMARK 465 SER A 8
REMARK 465 GLY A 9
REMARK 465 GLY A 10
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 LYS A 114 NZ
REMARK 470 GLU A 296 OE1 OE2
REMARK 470 GLU A 383 OE1 OE2
REMARK 470 LYS A 432 NZ
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 73 CD GLU A 73 OE2 0.082
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 ALA A 65 -124.52 50.66
REMARK 500 TRP A 133 -5.11 89.29
REMARK 500 TYR A 143 22.25 -150.56
REMARK 500 ASN A 209 105.54 -160.02
REMARK 500 GLN A 273 -61.84 -99.19
REMARK 500 ASP A 413 53.50 -93.39
REMARK 500 TRP A 452 -130.33 52.49
REMARK 500 ASP A 469 58.47 -142.15
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 TRS A 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1002
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1003
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1004
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1005
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1006
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1007
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3GNP RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A RICE OS3BGLU6 BETA-GLUCOSIDASE WITH OCTYL-
REMARK 900 BETA-D-THIO-GLUCOSIDE
REMARK 900 RELATED ID: 3GNR RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A RICE OS3BGLU6 BETA-GLUCOSIDASE WITH
REMARK 900 COVALENTLY BOUND 2-DEOXY-2-FLUOROGLUCOSIDE TO THE CATALYTIC
REMARK 900 NUCLEOPHILE E396
DBREF 3GNO A 5 488 UNP Q8L7J2 Q8L7J2_ORYSJ 38 521
SEQADV 3GNO SER A 1 UNP Q8L7J2 EXPRESSION TAG
SEQADV 3GNO PHE A 2 UNP Q8L7J2 EXPRESSION TAG
SEQADV 3GNO THR A 3 UNP Q8L7J2 EXPRESSION TAG
SEQADV 3GNO MET A 4 UNP Q8L7J2 EXPRESSION TAG
SEQRES 1 A 488 SER PHE THR MET ALA GLN GLN SER GLY GLY GLY LEU THR
SEQRES 2 A 488 ARG GLY SER PHE PRO GLU GLY PHE VAL PHE GLY THR ALA
SEQRES 3 A 488 SER ALA ALA TYR GLN TYR GLU GLY ALA VAL LYS GLU ASP
SEQRES 4 A 488 GLY ARG GLY GLN THR ILE TRP ASP THR PHE ALA HIS THR
SEQRES 5 A 488 PHE GLY LYS ILE THR ASP PHE SER ASN ALA ASP VAL ALA
SEQRES 6 A 488 VAL ASP GLN TYR HIS ARG PHE GLU GLU ASP ILE GLN LEU
SEQRES 7 A 488 MET ALA ASP MET GLY MET ASP ALA TYR ARG PHE SER ILE
SEQRES 8 A 488 ALA TRP SER ARG ILE TYR PRO ASN GLY VAL GLY GLN VAL
SEQRES 9 A 488 ASN GLN ALA GLY ILE ASP HIS TYR ASN LYS LEU ILE ASP
SEQRES 10 A 488 ALA LEU LEU ALA LYS GLY ILE GLN PRO TYR VAL THR LEU
SEQRES 11 A 488 TYR HIS TRP ASP LEU PRO GLN ALA LEU GLU ASP LYS TYR
SEQRES 12 A 488 LYS GLY TRP LEU ASP ARG GLN ILE VAL ASP ASP PHE ALA
SEQRES 13 A 488 ALA TYR ALA GLU THR CYS PHE ARG GLU PHE GLY ASP ARG
SEQRES 14 A 488 VAL LYS HIS TRP ILE THR LEU ASN GLU PRO HIS THR VAL
SEQRES 15 A 488 ALA ILE GLN GLY TYR ASP ALA GLY LEU GLN ALA PRO GLY
SEQRES 16 A 488 ARG CYS SER VAL LEU LEU HIS LEU TYR CYS LYS ALA GLY
SEQRES 17 A 488 ASN SER GLY THR GLU PRO TYR VAL VAL ALA HIS HIS PHE
SEQRES 18 A 488 ILE LEU ALA HIS ALA ALA ALA ALA SER ILE TYR ARG THR
SEQRES 19 A 488 LYS TYR LYS ALA THR GLN ASN GLY GLN LEU GLY ILE ALA
SEQRES 20 A 488 PHE ASP VAL MET TRP PHE GLU PRO MET SER ASN THR THR
SEQRES 21 A 488 ILE ASP ILE GLU ALA ALA LYS ARG ALA GLN GLU PHE GLN
SEQRES 22 A 488 LEU GLY TRP PHE ALA ASP PRO PHE PHE PHE GLY ASP TYR
SEQRES 23 A 488 PRO ALA THR MET ARG ALA ARG VAL GLY GLU ARG LEU PRO
SEQRES 24 A 488 ARG PHE THR ALA ASP GLU ALA ALA VAL VAL LYS GLY ALA
SEQRES 25 A 488 LEU ASP PHE VAL GLY ILE ASN HIS TYR THR THR TYR TYR
SEQRES 26 A 488 THR ARG HIS ASN ASN THR ASN ILE ILE GLY THR LEU LEU
SEQRES 27 A 488 ASN ASN THR LEU ALA ASP THR GLY THR VAL SER LEU PRO
SEQRES 28 A 488 PHE LYS ASN GLY LYS PRO ILE GLY ASP ARG ALA ASN SER
SEQRES 29 A 488 ILE TRP LEU TYR ILE VAL PRO ARG GLY MET ARG SER LEU
SEQRES 30 A 488 MET ASN TYR VAL LYS GLU ARG TYR ASN SER PRO PRO VAL
SEQRES 31 A 488 TYR ILE THR GLU ASN GLY MET ASP ASP SER ASN ASN PRO
SEQRES 32 A 488 PHE ILE SER ILE LYS ASP ALA LEU LYS ASP SER LYS ARG
SEQRES 33 A 488 ILE LYS TYR HIS ASN ASP TYR LEU THR ASN LEU ALA ALA
SEQRES 34 A 488 SER ILE LYS GLU ASP GLY CYS ASP VAL ARG GLY TYR PHE
SEQRES 35 A 488 ALA TRP SER LEU LEU ASP ASN TRP GLU TRP ALA ALA GLY
SEQRES 36 A 488 TYR SER SER ARG PHE GLY LEU TYR PHE VAL ASP TYR LYS
SEQRES 37 A 488 ASP ASN LEU LYS ARG TYR PRO LYS ASN SER VAL GLN TRP
SEQRES 38 A 488 PHE LYS ALA LEU LEU LYS THR
HET TRS A1001 16
HET GOL A1002 6
HET GOL A1003 6
HET GOL A1004 6
HET GOL A1005 6
HET GOL A1006 6
HET GOL A1007 6
HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
HETNAM GOL GLYCEROL
HETSYN TRS TRIS BUFFER
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 TRS C4 H12 N O3 1+
FORMUL 3 GOL 6(C3 H8 O3)
FORMUL 9 HOH *466(H2 O)
HELIX 1 1 THR A 13 PHE A 17 5 5
HELIX 2 2 ALA A 28 GLU A 33 1 6
HELIX 3 3 THR A 44 HIS A 51 1 8
HELIX 4 4 ASP A 67 ASP A 81 1 15
HELIX 5 5 ALA A 92 TYR A 97 1 6
HELIX 6 6 ASN A 105 LYS A 122 1 18
HELIX 7 7 PRO A 136 LYS A 144 1 9
HELIX 8 8 GLY A 145 ASP A 148 5 4
HELIX 9 9 ARG A 149 GLY A 167 1 19
HELIX 10 10 GLU A 178 ASP A 188 1 11
HELIX 11 11 THR A 212 TYR A 236 1 25
HELIX 12 12 TYR A 236 ASN A 241 1 6
HELIX 13 13 THR A 259 LEU A 274 1 16
HELIX 14 14 LEU A 274 GLY A 284 1 11
HELIX 15 15 PRO A 287 GLY A 295 1 9
HELIX 16 16 GLU A 296 LEU A 298 5 3
HELIX 17 17 THR A 302 LYS A 310 1 9
HELIX 18 18 ASN A 340 THR A 345 1 6
HELIX 19 19 PRO A 371 ASN A 386 1 16
HELIX 20 20 SER A 406 LEU A 411 1 6
HELIX 21 21 ASP A 413 GLU A 433 1 21
HELIX 22 22 GLU A 451 TYR A 456 5 6
HELIX 23 23 LYS A 476 LYS A 487 1 12
SHEET 1 A 9 VAL A 22 ALA A 26 0
SHEET 2 A 9 ALA A 86 SER A 90 1 O ARG A 88 N THR A 25
SHEET 3 A 9 GLN A 125 TYR A 131 1 O THR A 129 N PHE A 89
SHEET 4 A 9 HIS A 172 ASN A 177 1 O ILE A 174 N VAL A 128
SHEET 5 A 9 GLN A 243 ASP A 249 1 O GLY A 245 N THR A 175
SHEET 6 A 9 PHE A 315 ASN A 319 1 O ASN A 319 N PHE A 248
SHEET 7 A 9 VAL A 390 ASN A 395 1 O TYR A 391 N ILE A 318
SHEET 8 A 9 VAL A 438 TRP A 444 1 O ARG A 439 N VAL A 390
SHEET 9 A 9 VAL A 22 ALA A 26 1 N ALA A 26 O ALA A 443
SHEET 1 B 3 TRP A 252 PRO A 255 0
SHEET 2 B 3 THR A 323 HIS A 328 1 O TYR A 324 N GLU A 254
SHEET 3 B 3 THR A 347 LEU A 350 -1 O LEU A 350 N TYR A 325
SHEET 1 C 2 PHE A 352 LYS A 353 0
SHEET 2 C 2 LYS A 356 PRO A 357 -1 O LYS A 356 N LYS A 353
SHEET 1 D 2 ASP A 399 SER A 400 0
SHEET 2 D 2 SER A 458 ARG A 459 -1 O ARG A 459 N ASP A 399
SHEET 1 E 2 TYR A 463 VAL A 465 0
SHEET 2 E 2 ARG A 473 PRO A 475 -1 O TYR A 474 N PHE A 464
SSBOND 1 CYS A 197 CYS A 205 1555 1555 2.02
CISPEP 1 ALA A 193 PRO A 194 0 2.99
CISPEP 2 TRP A 444 SER A 445 0 1.17
SITE 1 AC1 12 GLN A 31 HIS A 132 GLU A 178 TYR A 321
SITE 2 AC1 12 TRP A 366 GLU A 394 TRP A 444 GLU A 451
SITE 3 AC1 12 TRP A 452 HOH A 672 HOH A 738 HOH A 948
SITE 1 AC2 4 ASP A 58 TYR A 467 HOH A 602 HOH A 801
SITE 1 AC3 4 PRO A 351 ILE A 365 TYR A 368 HOH A 919
SITE 1 AC4 6 ALA A 80 GLY A 83 MET A 84 ASP A 85
SITE 2 AC4 6 LYS A 122 HOH A 930
SITE 1 AC5 3 LYS A 408 LEU A 411 TYR A 474
SITE 1 AC6 5 ASP A 168 LYS A 171 THR A 239 GLN A 240
SITE 2 AC6 5 HOH A 808
SITE 1 AC7 10 ASN A 401 ASN A 402 PRO A 403 ILE A 405
SITE 2 AC7 10 ARG A 459 PHE A 464 LYS A 468 HOH A 547
SITE 3 AC7 10 HOH A 797 HOH A 837
CRYST1 56.809 90.489 101.710 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 0.017603 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011051 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009832 0.00000