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- PDB-3x2m: X-ray structure of PcCel45A with cellopentaose at 0.64 angstrom r... -

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Basic information

Entry
Database: PDB / ID: 3x2m
TitleX-ray structure of PcCel45A with cellopentaose at 0.64 angstrom resolution.
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
beta-cellopentaose / Endoglucanase V-like protein
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.64 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 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Other
Revision 1.2Dec 30, 2015Group: Experimental preparation
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.type / _citation.journal_abbrev ..._chem_comp.type / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)19,8363
Polymers18,1791
Non-polymers1,6572
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.938, 57.554, 63.431
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: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / pH: 8
Details: 60% 3-methyl-1,5-pentanediol, 50mM Tris-HCl, 5mM cellopentaose, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.71
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 0.64→50 Å / Num. obs: 313284 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 62.3
Reflection shellResolution: 0.64→0.65 Å / Redundancy: 2 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.2 / % possible all: 68.4

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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: 0.64→37.206 Å / SU ML: 0.06 / σ(F): 1.48 / Phase error: 12.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1289 15889 5.07 %
Rwork0.1221 --
obs0.1224 313240 91.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.64→37.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 112 280 1665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071584
X-RAY DIFFRACTIONf_angle_d1.3072189
X-RAY DIFFRACTIONf_dihedral_angle_d11.999592
X-RAY DIFFRACTIONf_chiral_restr0.3252
X-RAY DIFFRACTIONf_plane_restr0.008285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.6399-0.64720.33354100.35086961X-RAY DIFFRACTION65
0.6472-0.65480.33034250.33148278X-RAY DIFFRACTION77
0.6548-0.66280.3245090.31188765X-RAY DIFFRACTION81
0.6628-0.67110.28124610.2898990X-RAY DIFFRACTION83
0.6711-0.680.2824700.27349195X-RAY DIFFRACTION85
0.68-0.68930.24664810.26129406X-RAY DIFFRACTION87
0.6893-0.69910.23935060.23999476X-RAY DIFFRACTION88
0.6991-0.70960.2264720.22349599X-RAY DIFFRACTION89
0.7096-0.72070.20685700.20429523X-RAY DIFFRACTION89
0.7207-0.73250.20235310.18689797X-RAY DIFFRACTION91
0.7325-0.74510.17465220.17159821X-RAY DIFFRACTION91
0.7451-0.75870.16575350.15739890X-RAY DIFFRACTION91
0.7587-0.77330.1475280.14539950X-RAY DIFFRACTION92
0.7733-0.7890.135300.13849925X-RAY DIFFRACTION92
0.789-0.80620.13945090.133310171X-RAY DIFFRACTION93
0.8062-0.8250.12465420.126410118X-RAY DIFFRACTION93
0.825-0.84560.12085790.119610104X-RAY DIFFRACTION93
0.8456-0.86840.12675310.114910233X-RAY DIFFRACTION94
0.8684-0.8940.11255750.106810214X-RAY DIFFRACTION94
0.894-0.92290.10615390.100310269X-RAY DIFFRACTION94
0.9229-0.95580.09215500.096910284X-RAY DIFFRACTION95
0.9558-0.99410.0885550.095110213X-RAY DIFFRACTION94
0.9941-1.03940.10215690.089710211X-RAY DIFFRACTION94
1.0394-1.09420.09065170.08810320X-RAY DIFFRACTION94
1.0942-1.16270.09025180.085810400X-RAY DIFFRACTION95
1.1627-1.25250.0995890.093910709X-RAY DIFFRACTION98
1.2525-1.37860.10246230.101410918X-RAY DIFFRACTION100
1.3786-1.5780.10565550.103511041X-RAY DIFFRACTION100
1.578-1.98820.10496080.105411110X-RAY DIFFRACTION100
1.9882-37.26870.14815800.123411460X-RAY DIFFRACTION100

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