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- PDB-5mcd: Radiation damage to GH7 Family Cellobiohydrolase from Daphnia pul... -

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Basic information

Entry
Database: PDB / ID: 5mcd
TitleRadiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 3.27 MGy
ComponentsCellobiohydrolase CHBI
KeywordsHYDROLASE / Glycoside hydrolase / Cellobiohydrolase / radiation damage
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / glucan catabolic process / cellulose catabolic process
Similarity search - Function
1,4-Beta-D-Glucan Cellobiohydrolase I; Chain A / Glycoside hydrolase, family 7, domain / Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
cellulose 1,4-beta-cellobiosidase (non-reducing end)
Similarity search - Component
Biological speciesDaphnia pulex (common water flea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBury, C.S. / McGeehan, J.E. / Ebrahim, A. / Garman, E.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: J Synchrotron Radiat / Year: 2017
Title: OH cleavage from tyrosine: debunking a myth.
Authors: Bury, C.S. / Carmichael, I. / Garman, E.F.
History
DepositionNov 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellobiohydrolase CHBI
B: Cellobiohydrolase CHBI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8336
Polymers96,4602
Non-polymers3724
Water10,359575
1
A: Cellobiohydrolase CHBI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3222
Polymers48,2301
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellobiohydrolase CHBI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5104
Polymers48,2301
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.992, 46.646, 172.872
Angle α, β, γ (deg.)90.000, 108.260, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cellobiohydrolase CHBI


Mass: 48230.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daphnia pulex (common water flea) / Gene: CEL7A, DAPPUDRAFT_347598 / Production host: Trichoderma reesei QM6a (fungus)
References: UniProt: E9G5J5, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 % / Mosaicity: 0 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 900mM ammonium sulphate, 100mM monosodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→82.09 Å / Num. obs: 65572 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.037 / Rrim(I) all: 0.068 / Net I/σ(I): 12.2 / Num. measured all: 215330 / Scaling rejects: 215
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.053.40.2690.9441100
9.17-82.0930.0350.981199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.4data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4XNN

4xnn


Resolution: 2→82.085 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.71
RfactorNum. reflection% reflection
Rfree0.2016 3225 4.92 %
Rwork0.1798 --
obs0.1808 65539 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.62 Å2 / Biso mean: 27.3576 Å2 / Biso min: 10.95 Å2
Refinement stepCycle: final / Resolution: 2→82.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 23 575 7298
Biso mean--44.27 35.54 -
Num. residues----883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076901
X-RAY DIFFRACTIONf_angle_d1.2619367
X-RAY DIFFRACTIONf_chiral_restr0.0721005
X-RAY DIFFRACTIONf_plane_restr0.0051243
X-RAY DIFFRACTIONf_dihedral_angle_d12.362432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02990.281440.235627032847100
2.0299-2.06160.24781480.229126612809100
2.0616-2.09540.22951320.228126692801100
2.0954-2.13150.27131350.214227212856100
2.1315-2.17030.26421370.210526482785100
2.1703-2.2120.2621480.207427262874100
2.212-2.25720.24221360.206726872823100
2.2572-2.30630.22981470.203826842831100
2.3063-2.35990.23041430.198826622805100
2.3599-2.41890.23521440.206127122856100
2.4189-2.48430.21891440.19182646279099
2.4843-2.55750.21961500.200127092859100
2.5575-2.640.20851680.197526492817100
2.64-2.73440.25021390.19232701284099
2.7344-2.84390.25431340.183726962830100
2.8439-2.97330.19491400.185727292869100
2.9733-3.13010.18641330.180927202853100
3.1301-3.32620.18541210.165527422863100
3.3262-3.5830.16751420.157527372879100
3.583-3.94350.14931280.150127282856100
3.9435-4.51410.17241390.146827462885100
4.5141-5.68720.16551370.156127652902100
5.6872-82.15410.19751360.1912873300999

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