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- PDB-3x2p: Neutron and X-ray joint refined structure of PcCel45A with cellop... -

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Basic information

Entry
Database: PDB / ID: 3x2p
TitleNeutron and X-ray joint refined structure of PcCel45A with cellopentaose at 298K.
ComponentsEndoglucanase V-like protein
KeywordsHYDROLASE
Function / homology
Function and homology information


Expansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-cellopentaose / DEUTERATED WATER / Endoglucanase V-like protein
Similarity search - Component
Biological speciesPhanerochaete chrysosporium (fungus)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.518 Å
AuthorsNakamura, A. / Ishida, T. / Kusaka, K. / Yamada, T. / Tanaka, I. / Niimura, N. / 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3May 16, 2018Group: Data collection
Category: diffrn_detector / diffrn_radiation ...diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_detector.detector / _diffrn_radiation.wavelength_id ..._diffrn_detector.detector / _diffrn_radiation.wavelength_id / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.source / _diffrn_source.type
Revision 1.4Dec 18, 2019Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _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 / 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_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _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_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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)19,0082
Polymers18,1791
Non-polymers8291
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.478, 58.635, 64.744
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)-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
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 60% 3-methyl-1,5-pentanediol, 50mM Tris-HCl, 2.5mM Cellopentaose, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SPALLATION SOURCEORNL Spallation Neutron Source MANDI11.5-20.4
SYNCHROTRONPhoton Factory BL-5A21
Detector
TypeIDDetectorDate
IBIX (BL03), J-PARC1STORAGE PHOSPHORSMay 11, 2014
ADSC QUANTUM 315r2CCDJun 9, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NEUTRON TIME-OF-FLIGHTLAUELneutron1
2SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.51
220.41
311
Reflection

Entry-ID: 3X2P

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.5-37.82565194.14.30.2613.5
0.99-509754198.5016.30.0732110
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.552.20.4821.3184
0.99-1.015.90.3415.2292.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
STARGAZERdata reduction
STARGAZERdata scaling
Refinement

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)Biso max (Å2)Biso mean (Å2)Biso min (Å2)SU MLPhase error
1.518-19.685NEUTRON DIFFRACTION0.25970.21840.2192524256242.0491.5410
0.99-37.757X-RAY DIFFRACTION0.14230.13380.13391969974722.0298.4621.52119.4428.71866.850.0712.19
Refinement stepCycle: LAST / Resolution: 1.518→19.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 56 149 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0082900
NEUTRON DIFFRACTIONf_angle_d1.2384843
NEUTRON DIFFRACTIONf_dihedral_angle_d22.928769
NEUTRON DIFFRACTIONf_chiral_restr0.08227
NEUTRON DIFFRACTIONf_plane_restr0.006628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5183-1.6710.36261140.33515106NEUTRON DIFFRACTION76
1.671-1.91270.32521320.27536385NEUTRON DIFFRACTION94
1.9127-2.40910.24211360.19986704NEUTRON DIFFRACTION98
2.4091-19.68680.17041420.13126905NEUTRON DIFFRACTION98
0.99-1.01470.20191310.20396380X-RAY DIFFRACTION93
1.0147-1.04220.18111370.16736609X-RAY DIFFRACTION96
1.0422-1.07280.15281380.14266644X-RAY DIFFRACTION97
1.0728-1.10750.13161400.1286713X-RAY DIFFRACTION97
1.1075-1.14710.11881410.11756736X-RAY DIFFRACTION98
1.1471-1.1930.13841400.11816765X-RAY DIFFRACTION98
1.193-1.24730.14691380.12346835X-RAY DIFFRACTION99
1.2473-1.3130.15261380.12616801X-RAY DIFFRACTION99
1.313-1.39530.15181420.12926871X-RAY DIFFRACTION100
1.3953-1.5030.12711430.13156942X-RAY DIFFRACTION100
1.503-1.65430.16331420.1386927X-RAY DIFFRACTION100
1.6543-1.89370.14911450.14196981X-RAY DIFFRACTION100
1.8937-2.38580.14881440.13487020X-RAY DIFFRACTION100
2.3858-37.7840.1321500.13147279X-RAY DIFFRACTION100

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