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- PDB-6mvi: Apo Cel45A from Neurospora crassa OR74A -

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Basic information

Entry
Database: PDB / ID: 6mvi
TitleApo Cel45A from Neurospora crassa OR74A
ComponentsEndoglucanase V
KeywordsHYDROLASE / Endoglucanase V Glycoside hydrolase 45 family A
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 45 / Glycosyl hydrolase family 45 / Glycosyl hydrolases family 45 active site. / RlpA-like domain / RlpA-like domain superfamily / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. ...Glycoside hydrolase, family 45 / Glycosyl hydrolase family 45 / Glycosyl hydrolases family 45 active site. / RlpA-like domain / RlpA-like domain superfamily / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKadowaki, M.A.S. / Polikarpov, I.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Other government20111/20505-4 Brazil
CitationJournal: Biochimie / Year: 2019
Title: Structural insights into the hydrolysis pattern and molecular dynamics simulations of GH45 subfamily a endoglucanase from Neurospora crassa OR74A.
Authors: Kadowaki, M.A.S. / Polikarpov, I.
History
DepositionOct 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoglucanase V


Theoretical massNumber of molelcules
Total (without water)30,2821
Polymers30,2821
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.817, 72.975, 86.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoglucanase V


Mass: 30282.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: gh45-1, NCU05121 / Plasmid: pEXPYR / Production host: Aspergillus nidulans FGSC A4 (mold) / Variant (production host): A773 / References: UniProt: Q1K5M0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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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: 1.63 Å3/Da / Density % sol: 23.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM HEPES pH 8.0, 20% PEG6000 (w/w) and 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.89→36.49 Å / Num. obs: 16371 / % possible obs: 98.3 % / Redundancy: 7.4 % / CC1/2: 0.987 / Rrim(I) all: 0.207 / Net I/σ(I): 6.6
Reflection shellResolution: 1.89→1.96 Å / Mean I/σ(I) obs: 1.2 / CC1/2: 0.535 / Rrim(I) all: 0.993 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
APEX 2data reduction
APEX 2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GLX

5glx


Resolution: 1.89→36.487 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.61
RfactorNum. reflection% reflection
Rfree0.2311 1610 10.03 %
Rwork0.1674 --
obs0.1738 16054 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→36.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 0 221 1778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061626
X-RAY DIFFRACTIONf_angle_d0.8312220
X-RAY DIFFRACTIONf_dihedral_angle_d2.7131270
X-RAY DIFFRACTIONf_chiral_restr0.049225
X-RAY DIFFRACTIONf_plane_restr0.007299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.94560.25291260.20651150X-RAY DIFFRACTION96
1.9456-2.00840.2281310.1931156X-RAY DIFFRACTION97
2.0084-2.08020.28351300.18151193X-RAY DIFFRACTION98
2.0802-2.16350.27581300.17161148X-RAY DIFFRACTION98
2.1635-2.26190.24781340.16131199X-RAY DIFFRACTION99
2.2619-2.38110.22561340.16151193X-RAY DIFFRACTION99
2.3811-2.53030.24921350.16211195X-RAY DIFFRACTION99
2.5303-2.72560.23971360.17261211X-RAY DIFFRACTION99
2.7256-2.99980.23991350.17491213X-RAY DIFFRACTION99
2.9998-3.43360.25741360.17181236X-RAY DIFFRACTION99
3.4336-4.32480.18161390.14171242X-RAY DIFFRACTION99
4.3248-36.49430.18421440.15921308X-RAY DIFFRACTION98

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