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- PDB-5kjo: X-ray structure of PcCel45A expressed in Aspergillus nidullans -

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Basic information

Entry
Database: PDB / ID: 5kjo
TitleX-ray structure of PcCel45A expressed in Aspergillus nidullans
ComponentsEndoglucanase V-like protein
KeywordsHYDROLASE / endoglucanase / pccel45a / GH45 family / Phanerochaete chrysosporium / expansin
Function / homologyExpansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta / Endoglucanase V-like protein
Function and homology information
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsGodoy, A.S. / Ramia, M.P. / Camilo, C.M. / Polikarpov, I.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2008/56255-9, 2009/52840-7, 2009/05328-9, 2011/19100-0 and 2011/20505-4 Brazil
CitationJournal: To Be Published
Title: X-ray structure of PcCel45A expressed in Aspergillus nidullans
Authors: Godoy, A.S. / Ramia, M.P. / Camilo, C.M. / Polikarpov, I.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4275
Polymers18,1791
Non-polymers2484
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint12 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.624, 58.588, 63.675
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-like protein


Mass: 18178.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Gene: egv / Production host: Aspergillus nidulans FGSC A4 (mold) / References: UniProt: B3Y002
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.5 M Ammonium sulfate; 0.1 M Hepes pH 7.5; 30% v/v (+/-) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97924 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.47→31.8 Å / Num. obs: 29354 / % possible obs: 98.2 % / Redundancy: 7.4 % / Net I/σ(I): 12.5
Reflection shellHighest resolution: 1.47 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 3 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WC2

1wc2


Resolution: 1.47→31.8 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.58
RfactorNum. reflection% reflection
Rfree0.1724 2737 5 %
Rwork0.1423 --
obs0.1438 54736 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 16 236 1525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051336
X-RAY DIFFRACTIONf_angle_d0.7721818
X-RAY DIFFRACTIONf_dihedral_angle_d11.75463
X-RAY DIFFRACTIONf_chiral_restr0.076186
X-RAY DIFFRACTIONf_plane_restr0.005247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4671-1.49240.3496780.32131517X-RAY DIFFRACTION57
1.4924-1.51950.19071400.16822725X-RAY DIFFRACTION99
1.5195-1.54870.16311410.13522647X-RAY DIFFRACTION100
1.5487-1.58030.17251390.1322655X-RAY DIFFRACTION99
1.5803-1.61470.20251410.13452656X-RAY DIFFRACTION99
1.6147-1.65230.18391380.13542653X-RAY DIFFRACTION99
1.6523-1.69360.1731430.12952687X-RAY DIFFRACTION99
1.6936-1.73940.18711390.12632633X-RAY DIFFRACTION99
1.7394-1.79050.16771400.13092619X-RAY DIFFRACTION99
1.7905-1.84830.18381420.1312686X-RAY DIFFRACTION99
1.8483-1.91440.17541340.12992628X-RAY DIFFRACTION98
1.9144-1.9910.18621440.12862664X-RAY DIFFRACTION99
1.991-2.08160.17991430.12032640X-RAY DIFFRACTION99
2.0816-2.19130.15261350.12692644X-RAY DIFFRACTION99
2.1913-2.32860.16251370.13622680X-RAY DIFFRACTION99
2.3286-2.50830.15451390.1362627X-RAY DIFFRACTION99
2.5083-2.76060.16731420.1442656X-RAY DIFFRACTION99
2.7606-3.15980.19821370.14572666X-RAY DIFFRACTION99
3.1598-3.97980.14761440.13972669X-RAY DIFFRACTION100
3.9798-31.8450.17291410.1672647X-RAY DIFFRACTION99

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