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- PDB-3w9a: Crystal structure of the catalytic domain of the glycoside hydrol... -

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Basic information

Entry
Database: PDB / ID: 3w9a
TitleCrystal structure of the catalytic domain of the glycoside hydrolase family 131 protein from Coprinopsis cinerea
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / GH131 / beta-jelly roll
Function / homology
Function and homology information


cellulose binding / cellulose catabolic process / extracellular region / identical protein binding
Similarity search - Function
Jelly Rolls - #1160 / Glycoside hydrolase 131, catalytic N-terminal / Glycoside hydrolase 131 catalytic N-terminal domain / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CBM1 domain-containing protein
Similarity search - Component
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsMiyazaki, T. / Tanaka, Y. / Tamura, M. / Yoshida, M. / Nishikawa, A. / Tonozuka, T.
CitationJournal: Febs Lett. / Year: 2013
Title: Crystal structure of the N-terminal domain of a glycoside hydrolase family 131 protein from Coprinopsis cinerea
Authors: Miyazaki, T. / Yoshida, M. / Tamura, M. / Tanaka, Y. / Umezawa, K. / Nishikawa, A. / Tonozuka, T.
History
DepositionApr 1, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,67416
Polymers111,5694
Non-polymers1,10512
Water14,178787
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1684
Polymers27,8921
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1684
Polymers27,8921
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1684
Polymers27,8921
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1684
Polymers27,8921
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.200, 68.421, 69.168
Angle α, β, γ (deg.)89.99, 72.87, 85.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative uncharacterized protein / CcGH131A


Mass: 27892.197 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP residues 19-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Strain: Okayama-7 / Gene: CC1G_07166 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8NRB3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7% PEG4000, 100mM ammonium sulfate, 100mM sodium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.986→30.04 Å / Num. all: 66894 / Num. obs: 66894 / % possible obs: 94.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.105
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.289 / % possible all: 88.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AutoSolphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.99→30.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23587 3379 5.1 %RANDOM
Rwork0.18846 ---
obs0.19089 63505 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.854 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.99→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7575 0 72 787 8434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027879
X-RAY DIFFRACTIONr_bond_other_d00.026989
X-RAY DIFFRACTIONr_angle_refined_deg1.271.91810771
X-RAY DIFFRACTIONr_angle_other_deg3.668316023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7825945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79324.082392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.328151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3911540
X-RAY DIFFRACTIONr_chiral_restr0.0750.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219107
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022013
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.986→2.038 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 190 -
Rwork0.227 3730 -
obs--74.48 %

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