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- PDB-8bzq: Beta-1,4-D-endoglucanase Cel45A from Gloeophyllum trabeum -

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Basic information

Entry
Database: PDB / ID: 8bzq
TitleBeta-1,4-D-endoglucanase Cel45A from Gloeophyllum trabeum
ComponentsEndoglucanase V-like protein
KeywordsHYDROLASE / ENDOGLUCANASE / GTCEL45A / GH45 FAMILY / CELLULASE / BROWN ROT
Function / homologyExpansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / EXPB1-like domain 1 / RlpA-like domain superfamily / Endoglucanase V-like protein
Function and homology information
Biological speciesGloeophyllum trabeum ATCC 11539 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsOkmane, L. / Fitkin, L. / Stahlberg, J.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other government2017-01130 Sweden
CitationJournal: Febs Open Bio / Year: 2024
Title: The first crystal structure of a family 45 glycoside hydrolase from a brown-rot fungus, Gloeophyllum trabeum GtCel45A.
Authors: Okmane, L. / Fitkin, L. / Sandgren, M. / Stahlberg, J.
History
DepositionDec 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase V-like protein


Theoretical massNumber of molelcules
Total (without water)18,3931
Polymers18,3931
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.970, 48.410, 45.790
Angle α, β, γ (deg.)90.000, 92.207, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Endoglucanase V-like protein


Mass: 18392.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeophyllum trabeum ATCC 11539 (fungus)
Gene: GLOTRDRAFT_59933 / Production host: Aspergillus nidulans (mold) / Strain (production host): A773 / References: UniProt: S7QB86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.74 Å3/Da / Density % sol: 29.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES 7.5, 20% PEG 3350, 3mM NiCl2, protein 14 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.3→45.76 Å / Num. obs: 31123 / % possible obs: 99.7 % / Redundancy: 12.84 % / Biso Wilson estimate: 9.63 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.18 / Net I/σ(I): 8.9
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 9.51 / Num. unique obs: 3078 / CC1/2: 0.97 / Rrim(I) all: 0.187 / % possible all: 99.26

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KJO

5kjo


Resolution: 1.3→45.76 Å / SU ML: 0.063 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 17.1646
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1826 974 3.13 %
Rwork0.1657 30135 -
obs0.1663 31109 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.27 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 0 217 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551304
X-RAY DIFFRACTIONf_angle_d0.92581787
X-RAY DIFFRACTIONf_chiral_restr0.0801184
X-RAY DIFFRACTIONf_plane_restr0.0069245
X-RAY DIFFRACTIONf_dihedral_angle_d6.3723193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.370.17011440.16894248X-RAY DIFFRACTION99.28
1.37-1.450.19991400.16824285X-RAY DIFFRACTION99.68
1.45-1.570.17531440.16174305X-RAY DIFFRACTION99.87
1.57-1.720.17741340.16694291X-RAY DIFFRACTION99.95
1.72-1.970.19431420.16954306X-RAY DIFFRACTION100
1.97-2.490.20441350.17164328X-RAY DIFFRACTION99.91

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