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

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Basic information

Entry
Database: PDB / ID: 5mch
TitleRadiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 9.75 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 / 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)127.347, 46.722, 173.883
Angle α, β, γ (deg.)90.000, 108.250, 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: 2.55 Å3/Da / Density % sol: 51.7 % / 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→82.57 Å / Num. obs: 66183 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.05 / Rrim(I) all: 0.092 / Net I/σ(I): 8.3 / Num. measured all: 215589 / Scaling rejects: 271
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.053.40.7460.645199.9
9.38-82.5730.0330.981199.7

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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→82.568 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.86
RfactorNum. reflection% reflection
Rfree0.2247 3245 4.92 %
Rwork0.2061 --
obs0.207 66012 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.31 Å2 / Biso mean: 37.7742 Å2 / Biso min: 18.4 Å2
Refinement stepCycle: final / Resolution: 2→82.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 23 575 7298
Biso mean--59.19 47.6 -
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 (%)
2-2.02990.27561450.28532694283999
2.0299-2.06160.29661530.2862676282999
2.0616-2.09540.29341270.28042689281699
2.0954-2.13150.35371310.28222712284399
2.1315-2.17030.29371500.26932688283899
2.1703-2.2120.3031320.26732707283999
2.212-2.25720.28791470.26522707285499
2.2572-2.30630.30141420.25432676281899
2.3063-2.35990.25471520.24582701285399
2.3599-2.41890.26451460.24842724287099
2.4189-2.48440.28861400.248326952835100
2.4844-2.55750.27771430.249127142857100
2.5575-2.640.24461690.23926882857100
2.64-2.73440.27431500.23372727287799
2.7344-2.84390.27421340.220927132847100
2.8439-2.97330.24021400.224527592899100
2.9733-3.13010.2021360.211827452881100
3.1301-3.32620.22311150.199427752890100
3.3262-3.5830.19031480.17927692917100
3.583-3.94360.1741280.168827422870100
3.9436-4.51420.17921440.155827832927100
4.5142-5.68720.17961360.16427942930100
5.6872-82.63870.20271370.19772889302699

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