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- PDB-3x2l: X-ray structure of PcCel45A apo form at 95K. -

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Basic information

Entry
Database: PDB / ID: 3x2l
TitleX-ray structure of PcCel45A apo form at 95K.
ComponentsEndoglucanase V-like protein
KeywordsHYDROLASE
Function / homology
Function and homology information


Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / EXPB1-like domain 1 / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
3-methylpentane-1,5-diol / Endoglucanase V-like protein
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.83 Å
AuthorsNakamura, A. / Ishida, T. / Ohta, K. / Tanaka, H. / Inaka, K. / Samejima, M. / Igarashi, K.
CitationJournal: Sci Adv / Year: 2015
Title: "Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography.
Authors: Nakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Fushinobu, S. / Tanaka, I. / Kaneko, S. / Ohta, K. / Tanaka, H. / Inaka, K. / Higuchi, Y. / Niimura, N. / Samejima, M. / Igarashi, K.
History
DepositionDec 22, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Other
Revision 1.2Dec 30, 2015Group: Experimental preparation
Revision 1.3Dec 18, 2019Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Nov 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Endoglucanase V-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7746
Polymers18,1791
Non-polymers5955
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.450, 58.086, 62.862
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 / Fragment: UNP residues 27-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: egv, PcCel45A / Plasmid: pPICZa / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: B3Y002
#2: Chemical
ChemComp-40S / 3-methylpentane-1,5-diol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293 K / Method: liquid diffusion under micro gravity / pH: 8
Details: 60% 3-methyl-1,5-pentanediol, 50mM Tris-HCl, pH 8.0, Liquid diffusion under micro gravity, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.75 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 0.8→50 Å / Num. obs: 176380 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 15.1
Reflection shellResolution: 0.8→0.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3 / % possible all: 92.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.83→27.643 Å / SU ML: 0.04 / σ(F): 1.52 / Phase error: 8.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1248 7753 5.03 %
Rwork0.1151 --
obs0.1156 154250 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.83→27.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 40 214 1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071508
X-RAY DIFFRACTIONf_angle_d1.3032061
X-RAY DIFFRACTIONf_dihedral_angle_d17.045528
X-RAY DIFFRACTIONf_chiral_restr0.091206
X-RAY DIFFRACTIONf_plane_restr0.008287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8304-0.83980.20992550.19134586X-RAY DIFFRACTION94
0.8398-0.84970.17562530.17694667X-RAY DIFFRACTION95
0.8497-0.860.15022170.16374744X-RAY DIFFRACTION96
0.86-0.87090.142830.15434707X-RAY DIFFRACTION96
0.8709-0.88240.16112620.14814738X-RAY DIFFRACTION97
0.8824-0.89450.15612300.13884746X-RAY DIFFRACTION97
0.8945-0.90730.12742540.13014784X-RAY DIFFRACTION97
0.9073-0.92080.14042630.12154794X-RAY DIFFRACTION97
0.9208-0.93520.13152730.11414812X-RAY DIFFRACTION98
0.9352-0.95050.11632270.10754860X-RAY DIFFRACTION98
0.9505-0.96690.11542490.10174840X-RAY DIFFRACTION98
0.9669-0.98450.09792570.09774884X-RAY DIFFRACTION99
0.9845-1.00340.10072700.09384803X-RAY DIFFRACTION99
1.0034-1.02390.10442800.08874894X-RAY DIFFRACTION99
1.0239-1.04620.09672630.08674857X-RAY DIFFRACTION99
1.0462-1.07050.09252300.08354906X-RAY DIFFRACTION99
1.0705-1.09730.08042570.08224961X-RAY DIFFRACTION99
1.0973-1.1270.08652780.08064886X-RAY DIFFRACTION99
1.127-1.16010.08922650.08114901X-RAY DIFFRACTION99
1.1601-1.19760.09442690.08364913X-RAY DIFFRACTION99
1.1976-1.24040.0862480.08984961X-RAY DIFFRACTION100
1.2404-1.290.10662420.09554976X-RAY DIFFRACTION99
1.29-1.34870.10542620.10524938X-RAY DIFFRACTION99
1.3487-1.41990.11082690.10844960X-RAY DIFFRACTION99
1.4199-1.50880.11032800.10944924X-RAY DIFFRACTION99
1.5088-1.62530.11452580.10965008X-RAY DIFFRACTION100
1.6253-1.78880.13362600.11264984X-RAY DIFFRACTION99
1.7888-2.04760.14552640.12255074X-RAY DIFFRACTION100
2.0476-2.57950.14552620.12855094X-RAY DIFFRACTION100
2.5795-27.65880.1532730.14115295X-RAY DIFFRACTION100

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