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- PDB-3x2g: X-ray structure of PcCel45A N92D apo form at 100K -

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Basic information

Entry
Database: PDB / ID: 3x2g
TitleX-ray structure of PcCel45A N92D apo form at 100K
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 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

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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)18,6565
Polymers18,1801
Non-polymers4774
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.996, 45.612, 63.093
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: 18179.777 Da / Num. of mol.: 1 / Fragment: UNP residues 27-206 / Mutation: N92D
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.: 3 / 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.: 266 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 65% 3-methyl-1,5-pentanediol, 50 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 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→50 Å / Num. obs: 90937 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rsym value: 0.027 / Net I/σ(I): 43.5
Reflection shellResolution: 1→1.02 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 7.4 / Num. unique all: 8763 / Rsym value: 0.205 / % possible all: 100

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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→18.484 Å / SU ML: 0.04 / σ(F): 1.34 / Phase error: 6.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1093 9075 10.02 %
Rwork0.0971 --
obs0.0983 90553 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→18.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 32 266 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071437
X-RAY DIFFRACTIONf_angle_d1.3311957
X-RAY DIFFRACTIONf_dihedral_angle_d18.108494
X-RAY DIFFRACTIONf_chiral_restr0.077194
X-RAY DIFFRACTIONf_plane_restr0.008270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1-1.01150.12243060.1036266199
1.0115-1.02340.11673050.09642670100
1.0234-1.03590.10862940.09442706100
1.0359-1.0490.11183200.08532639100
1.049-1.06280.09612930.08412700100
1.0628-1.07740.09062990.07982711100
1.0774-1.09280.09683000.07952706100
1.0928-1.10910.08643010.07362694100
1.1091-1.12640.07963150.06932684100
1.1264-1.14490.08323090.07012697100
1.1449-1.16460.07573140.06532657100
1.1646-1.18580.07843100.06692704100
1.1858-1.20860.08883160.07122698100
1.2086-1.23320.08783100.0732707100
1.2332-1.26010.08573160.0752713100
1.2601-1.28940.08932930.07642681100
1.2894-1.32160.09663150.07842723100
1.3216-1.35730.10282720.07752703100
1.3573-1.39720.08353050.07812731100
1.3972-1.44230.09622670.08052780100
1.4423-1.49390.09463010.08472719100
1.4939-1.55360.09812900.08232723100
1.5536-1.62430.10012970.0882771100
1.6243-1.70990.11163340.09172707100
1.7099-1.81690.10073060.09482744100
1.8169-1.95710.11052940.09932750100
1.9571-2.15370.0993030.09772779100
2.1537-2.46480.13023060.11342777100
2.4648-3.1030.13243000.11992825100
3.103-18.48690.16452840.1501271892

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