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- PDB-3x2o: Neutron and X-ray joint refined structure of PcCel45A apo form at... -

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Basic information

Entry
Database: PDB / ID: 3x2o
TitleNeutron and X-ray joint refined structure of PcCel45A apo form at 298K.
ComponentsEndoglucanase V-like protein
KeywordsHYDROLASE
Function / homologyExpansin/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 / DEUTERATED WATER / Endoglucanase V-like protein
Function and homology information
Biological speciesPhanerochaete chrysosporium (fungus)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2May 16, 2018Group: Data collection
Category: diffrn_detector / diffrn_radiation ...diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_detector.detector / _diffrn_detector.pdbx_collection_date ..._diffrn_detector.detector / _diffrn_detector.pdbx_collection_date / _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 1.3Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_radiation / struct_conn
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase V-like protein


Theoretical massNumber of molelcules
Total (without water)18,1791
Polymers18,1791
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.152, 59.067, 64.285
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: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 60% 3-methyl-1,5-pentanediol, 50 mM Tris-HCl, pH 7.5, 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 PHOSPHORSApr 25, 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: 3X2O

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.5-20.42558193.33.90.24513.9
1-509918999.5013.10.082106
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.5-1.552.10.5011.4181.1
1-1.026.30.2996.5299.4

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Processing

Software
NameVersionClassification
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 (%)SU MLDiffraction-IDPhase errorBiso mean (Å2)σ(F)
1.5-18.826NEUTRON DIFFRACTION0.25060.22750.22982548254339.9694.220.23123.39
1-28.233X-RAY DIFFRACTION0.15310.13490.13679389941599.9799.260.05211.3527.48491.49
Refinement stepCycle: LAST / Resolution: 1.5→18.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 0 152 1413
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0082766
NEUTRON DIFFRACTIONf_angle_d1.2084694
NEUTRON DIFFRACTIONf_dihedral_angle_d16.335706
NEUTRON DIFFRACTIONf_chiral_restr0.088188
NEUTRON DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.55940.36341170.39061044NEUTRON DIFFRACTION79
1.5594-1.59120.37611090.35791150NEUTRON DIFFRACTION84
1.5912-1.62580.37861500.34681129NEUTRON DIFFRACTION87
1.6258-1.66360.34191430.32731181NEUTRON DIFFRACTION89
1.6636-1.70520.32541380.31531228NEUTRON DIFFRACTION91
1.7052-1.75130.31321250.30761257NEUTRON DIFFRACTION94
1.7513-1.80280.33521560.29051262NEUTRON DIFFRACTION95
1.8028-1.86090.28311450.25891313NEUTRON DIFFRACTION97
1.8609-1.92730.27751380.24711302NEUTRON DIFFRACTION96
1.9273-2.00440.22471430.22721305NEUTRON DIFFRACTION97
2.0044-2.09550.22471440.21761319NEUTRON DIFFRACTION98
2.0955-2.20590.22531420.19571354NEUTRON DIFFRACTION99
2.2059-2.34380.19281530.18111321NEUTRON DIFFRACTION99
2.3438-2.52440.18361490.17341354NEUTRON DIFFRACTION99
2.5244-2.77770.20091420.16121380NEUTRON DIFFRACTION100
2.7777-3.1780.18491560.15541375NEUTRON DIFFRACTION100
3.178-3.99760.1831500.15081390NEUTRON DIFFRACTION99
3.9976-18.82720.1941480.15431369NEUTRON DIFFRACTION92
1.0021-1.01340.18392990.1752596X-RAY DIFFRACTION93
1.0134-1.02540.16472820.16622842X-RAY DIFFRACTION99
1.0254-1.03790.16422890.15322805X-RAY DIFFRACTION99
1.0379-1.0510.15153240.1412794X-RAY DIFFRACTION99
1.051-1.06480.14053150.13382751X-RAY DIFFRACTION99
1.0648-1.07940.13832970.12952797X-RAY DIFFRACTION99
1.0794-1.09480.1353280.12312812X-RAY DIFFRACTION99
1.0948-1.11120.142940.11882803X-RAY DIFFRACTION99
1.1112-1.12860.13353090.11422807X-RAY DIFFRACTION99
1.1286-1.14710.12953220.11062795X-RAY DIFFRACTION99
1.1471-1.16680.12252850.10912830X-RAY DIFFRACTION99
1.1668-1.18810.12813330.11752781X-RAY DIFFRACTION100
1.1881-1.21090.1393050.11372825X-RAY DIFFRACTION100
1.2109-1.23560.12333160.12112811X-RAY DIFFRACTION100
1.2356-1.26250.14243250.11932795X-RAY DIFFRACTION100
1.2625-1.29190.14653060.12672819X-RAY DIFFRACTION99
1.2919-1.32420.13983240.12312774X-RAY DIFFRACTION99
1.3242-1.360.13422980.12212842X-RAY DIFFRACTION99
1.36-1.40.13313160.12212814X-RAY DIFFRACTION99
1.4-1.44520.14433390.12452803X-RAY DIFFRACTION99
1.4452-1.49680.13053080.12892818X-RAY DIFFRACTION99
1.4968-1.55670.13733170.12772831X-RAY DIFFRACTION100
1.5567-1.62760.14573190.12852846X-RAY DIFFRACTION100
1.6276-1.71340.13783290.13252859X-RAY DIFFRACTION100
1.7134-1.82070.15133080.14172857X-RAY DIFFRACTION100
1.8207-1.96130.14933150.13922879X-RAY DIFFRACTION100
1.9613-2.15860.14773120.1352896X-RAY DIFFRACTION100
2.1586-2.47080.13883200.14362911X-RAY DIFFRACTION100
2.4708-3.11230.1643240.13742946X-RAY DIFFRACTION100
3.1123-28.24420.17773310.143031X-RAY DIFFRACTION99

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