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- PDB-4zm7: PcCel45A N105D mutatnt at cryo condition -

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Basic information

Entry
Database: PDB / ID: 4zm7
TitlePcCel45A N105D mutatnt at cryo condition
ComponentsEndoglucanase V-like protein
KeywordsHYDROLASE / Cellulase Endo-glucanase
Function / homologyExpansin/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 / Endoglucanase V-like protein
Function and homology information
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.701 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
DepositionMay 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)18,1801
Polymers18,1801
Non-polymers00
Water8,449469
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7600 Å2
Unit cell
Length a, b, c (Å)45.764, 57.955, 63.079
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 / PcCel45A


Mass: 18179.777 Da / Num. of mol.: 1 / Fragment: UNP residues 27-206 / Mutation: N131D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Strain: K-3 / Gene: egv / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H / References: UniProt: B3Y002
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20 mM Tris-HCl, 65% 3-methyl-1,5-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.7→50 Å / Num. obs: 262663 / % possible obs: 95.1 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 90.4
Reflection shellResolution: 0.7→0.71 Å / Redundancy: 4 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 6.4 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.701→25.97 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 10.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1347 12658 5.07 %
Rwork0.1264 --
obs0.1268 249760 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.701→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 0 469 1729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071436
X-RAY DIFFRACTIONf_angle_d1.2691973
X-RAY DIFFRACTIONf_dihedral_angle_d11.549488
X-RAY DIFFRACTIONf_chiral_restr0.076204
X-RAY DIFFRACTIONf_plane_restr0.008277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.7006-0.70860.25613860.23867188X-RAY DIFFRACTION87
0.7086-0.71690.20344310.20517538X-RAY DIFFRACTION92
0.7169-0.72560.20014370.18237565X-RAY DIFFRACTION93
0.7256-0.73480.1653850.1667631X-RAY DIFFRACTION93
0.7348-0.74450.16254330.15657648X-RAY DIFFRACTION93
0.7445-0.75470.15754210.14787737X-RAY DIFFRACTION94
0.7547-0.76550.13564160.14377759X-RAY DIFFRACTION94
0.7655-0.77690.14373960.14227807X-RAY DIFFRACTION95
0.7769-0.7890.1414170.14347799X-RAY DIFFRACTION95
0.789-0.8020.14363970.14357867X-RAY DIFFRACTION95
0.802-0.81580.1444170.14317876X-RAY DIFFRACTION96
0.8158-0.83060.13634300.13477932X-RAY DIFFRACTION96
0.8306-0.84660.13444280.13397931X-RAY DIFFRACTION96
0.8466-0.86390.12714270.13097975X-RAY DIFFRACTION97
0.8639-0.88270.13094240.12627994X-RAY DIFFRACTION97
0.8827-0.90320.1234340.12618000X-RAY DIFFRACTION97
0.9032-0.92580.13384350.12038069X-RAY DIFFRACTION98
0.9258-0.95080.11894300.11418101X-RAY DIFFRACTION98
0.9508-0.97880.11734310.1148073X-RAY DIFFRACTION98
0.9788-1.01040.11674510.10938148X-RAY DIFFRACTION98
1.0104-1.04650.1134320.10648166X-RAY DIFFRACTION99
1.0465-1.08840.10154130.10058242X-RAY DIFFRACTION99
1.0884-1.1380.094330.0968212X-RAY DIFFRACTION99
1.138-1.1980.10654350.09948285X-RAY DIFFRACTION100
1.198-1.2730.11214520.10858293X-RAY DIFFRACTION100
1.273-1.37130.1084760.11258331X-RAY DIFFRACTION100
1.3713-1.50930.11954310.11698371X-RAY DIFFRACTION100
1.5093-1.72760.13774390.12158389X-RAY DIFFRACTION100
1.7276-2.17650.14844240.12898039X-RAY DIFFRACTION94
2.1765-25.98740.19732970.16696136X-RAY DIFFRACTION70

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