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

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Basic information

Entry
Database: PDB / ID: 5mcc
TitleRadiation damage to GH7 Family Cellobiohydrolase from Daphnia pulex: Dose (DWD) 1.11 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 13, 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)126.972, 46.640, 172.794
Angle α, β, γ (deg.)90.000, 108.280, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PCA / Beg label comp-ID: PCA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 20 - 464 / Label seq-ID: 1 - 445

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 51.16 % / 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→164.07 Å / Num. obs: 65500 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.053.40.2390.954199.9
9.17-164.0730.0320.993199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.4data scaling
PHASERphasing
REFMAC5.8.0155refinement
PHENIXrefinement
PDB_EXTRACT3.2data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4XNN

4xnn


Resolution: 2→164.07 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.86 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.12 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1728 3220 4.9 %RANDOM
Rwork0.1513 ---
obs0.1523 62235 99.7 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 114.04 Å2 / Biso mean: 30.18 Å2 / Biso min: 12.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0 Å2-0.4 Å2
2--2.45 Å2-0 Å2
3----1.5 Å2
Refinement stepCycle: final / Resolution: 2→164.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 23 575 7298
Biso mean--43 35.13 -
Num. residues----883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026901
X-RAY DIFFRACTIONr_bond_other_d0.0020.026084
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9359399
X-RAY DIFFRACTIONr_angle_other_deg0.888314060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07525.127316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.423151025
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.521526
X-RAY DIFFRACTIONr_chiral_restr0.0720.21009
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021591
X-RAY DIFFRACTIONr_mcbond_it1.7020.5743528
X-RAY DIFFRACTIONr_mcbond_other1.6940.5743527
X-RAY DIFFRACTIONr_mcangle_it2.2210.854403
Refine LS restraints NCS

Ens-ID: 1 / Number: 29324 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 250 -
Rwork0.177 4592 -
all-4842 -
obs--99.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6658-0.0109-0.80050.9676-0.53773.7192-0.0112-0.47470.04910.094-0.0422-0.0699-0.03710.65990.05340.178-0.031-0.03370.3171-0.00980.2145-19.79911.89636.884
21.0065-0.0383-0.26170.4919-0.0882.24750.0031-0.2640.02260.0916-0.0229-0.0348-0.01160.26810.01990.1946-0.00540.00520.09660.00390.187-29.25310.89828.933
31.3362-0.1239-0.02791.152-0.09271.62150.0140.05570.0324-0.0519-0.01940.08570.0485-0.07930.00540.20620.00850.01230.01610.0040.1561-38.8027.88912.762
41.55940.2831-0.27726.7582-3.15173.26020.0092-0.1261-0.1382-0.2551-0.157-0.25290.29210.32530.14780.19990.0402-0.01040.12790.01940.1752-24.1154.80517.184
51.38730.36810.58990.90680.0494.2145-0.0405-0.08630.1004-0.0710.04930.0073-0.5580.1324-0.00880.2694-0.04970.03410.2086-0.02820.2018-48.69239.24348.581
60.9910.0115-0.08570.71430.09812.91320.0647-0.2082-0.0603-0.03610.0009-0.0761-0.03330.1604-0.06570.1866-0.0140.0170.2342-0.01610.1627-48.88129.81257.369
73.17380.17610.0340.6672-0.66073.6896-0.0150.05870.1124-0.04160.12660.1341-0.1248-0.4662-0.11150.2075-0.00470.00750.2343-0.01980.1906-60.40629.74343.002
81.44360.20710.11940.75620.19552.91070.0309-0.3736-0.1760.03340.01240.03050.2049-0.4604-0.04330.1946-0.04020.01010.42050.04980.1658-62.50124.86667.133
92.81461.4209-1.68694.9012-3.2325.8636-0.10510.05920.2638-0.22980.39870.5875-0.1335-1.1734-0.29360.24540.0526-0.02430.70840.03420.2496-75.81134.861.781
103.2577-1.77532.29923.5933-2.36644.8727-0.1961-0.50.1540.17050.28150.1171-0.567-0.4725-0.08540.2852-0.02750.03920.3889-0.03670.1568-55.73439.15964.938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 92
2X-RAY DIFFRACTION2A93 - 284
3X-RAY DIFFRACTION3A285 - 437
4X-RAY DIFFRACTION4A438 - 464
5X-RAY DIFFRACTION5B21 - 134
6X-RAY DIFFRACTION6B135 - 191
7X-RAY DIFFRACTION7B192 - 235
8X-RAY DIFFRACTION8B236 - 401
9X-RAY DIFFRACTION9B402 - 437
10X-RAY DIFFRACTION10B438 - 464

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