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- PDB-3x2j: X-ray structure of PcCel45A D114N apo form at 95K. -

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Basic information

Entry
Database: PDB / ID: 3x2j
TitleX-ray structure of PcCel45A D114N 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: 1.301 Å
AuthorsNakamura, A. / Ishida, T. / 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 7, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Oct 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_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)18,2962
Polymers18,1781
Non-polymers1181
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.802, 43.998, 60.677
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: 18177.809 Da / Num. of mol.: 1 / Fragment: UNP residues 27-206 / Mutation: D114N
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.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 65% 3-methyl-1,5-pentanediol, 50 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 39373 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 44.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 5.9 / Num. unique all: 3528 / % possible all: 92.7

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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: 1.301→26.459 Å / SU ML: 0.08 / σ(F): 1.37 / Phase error: 10.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1308 1999 5.1 %
Rwork0.1148 --
obs0.1156 39195 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.301→26.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 8 186 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141364
X-RAY DIFFRACTIONf_angle_d1.5161858
X-RAY DIFFRACTIONf_dihedral_angle_d13.448458
X-RAY DIFFRACTIONf_chiral_restr0.091189
X-RAY DIFFRACTIONf_plane_restr0.01258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3006-1.33310.13651460.09992612100
1.3331-1.36920.12581400.08842622100
1.3692-1.40950.11451420.08672656100
1.4095-1.4550.1051450.08612593100
1.455-1.5070.13151450.08562660100
1.507-1.56730.10651420.0842641100
1.5673-1.63860.12671420.0832646100
1.6386-1.7250.11741460.08412636100
1.725-1.8330.12071420.09532678100
1.833-1.97450.11411350.09492654100
1.9745-2.17320.11731440.0952687100
2.1732-2.48740.12581440.11492697100
2.4874-3.13310.12941420.13042723100
3.1331-26.4640.15981440.1581269194

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