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- PDB-4xnn: Crystal Structure of a GH7 Family Cellobiohydrolase from Daphnia pulex -

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Basic information

Entry
Database: PDB / ID: 4xnn
TitleCrystal Structure of a GH7 Family Cellobiohydrolase from Daphnia pulex
ComponentsCellobiohydrolase CHBI
KeywordsHYDROLASE / Cellulose 1 / 4-beta-Cellobiosidase / fresh water arthropod / cellulase / Cel7
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: 1.9 Å
AuthorsEbrahim, A. / Hobdey, S.E. / Podkaminer, K. / Taylor II, L.E. / Beckham, G.T. / Decker, S.R. / Himmel, M.E. / Cragg, S.M. / McGeehan, J.E.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L001926/1 United Kingdom
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Characterization of a GH7 Family Cellobiohydrolase from Daphnia pulex
Authors: Hobdey, S.E. / Ebrahim, A. / Podkaminer, K. / Taylor II, L.E. / Beckham, G.T. / Decker, S.R. / Himmel, M.E. / Cragg, S.M. / McGeehan, J.E.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / 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 / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 3.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.1Mar 30, 2022Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description / Source and taxonomy
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_refine_tls_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity_src_gen.gene_src_common_name / _pdbx_audit_support.funding_organization / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.end_auth_asym_id
Revision 3.2Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)96,6454
Polymers96,4602
Non-polymers1842
Water9,782543
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
MethodPISA
2
B: 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
MethodPISA
Unit cell
Length a, b, c (Å)128.290, 47.020, 173.500
Angle α, β, γ (deg.)90.000, 108.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cellobiohydrolase CHBI / GH7 family protein


Mass: 48230.168 Da / Num. of mol.: 2 / Fragment: UNP residues 20-464
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.26 % / Description: Thin plate, 110 um x 80 um
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 800mM ammonium sulphate, 100mM sodium citrate, 10mM sodium acetate, 50mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionNumber: 241715 / Rmerge(I) obs: 0.065 / Χ2: 1 / D res high: 1.9 Å / Num. obs: 136641 / % possible obs: 90
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
8.543.6131310.028
6.018.5251110.031
4.916.01345510.032
4.254.91390910.033
3.84.25450510.036
3.473.8523710.04
3.213.47592710.046
33.21621010.057
2.833693010.072
2.692.83712310.086
2.562.69772010.109
2.452.56814410.132
2.362.45815710.154
2.272.36854910.17
2.192.27892710.202
2.122.19878510.256
2.062.12945310.308
22.06981610.38
1.952971110.463
1.91.951025910.584
ReflectionResolution: 1.9→43.6 Å / Num. obs: 75459 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 1.76 % / Biso Wilson estimate: 34.459 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.091 / Χ2: 1.002 / Net I/σ(I): 7.85 / Num. measured all: 241715
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.950.5130.5841.461803011268102590.82691
1.95-20.6340.4631.83169721084397110.65489.6
2-2.060.7140.382.33172911070898160.53791.7
2.06-2.120.7810.3082.93166041036594530.43691.2
2.12-2.190.8290.2563.5515228997287850.36288.1
2.19-2.270.8940.2024.4415649973789270.28591.7
2.27-2.360.9170.175.2215182938285490.2491.1
2.36-2.450.9270.1545.8414287898081570.21890.8
2.45-2.560.9420.1326.8614527859381440.18694.8
2.56-2.690.9560.1098.0913722818977200.15594.3
2.69-2.830.9730.0869.6812572786971230.12290.5
2.83-30.9810.07211.0712497742669300.10293.3
3-3.210.9870.05712.8810966697662100.08189
3.21-3.470.9910.04615.3510602651259270.06591
3.47-3.80.9920.0417.259288599452370.05787.4
3.8-4.250.9930.03618.68092540845050.05183.3
4.25-4.910.9940.03319.316945473639090.04782.5
4.91-6.010.9940.03218.996249402234550.04585.9
6.01-8.50.9950.03119.194590311025110.04380.7
8.5-43.60.9950.02821.072422169813130.0477.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å43.87 Å
Translation1.9 Å43.87 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YG1

2yg1


Resolution: 1.9→43.6 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2016 / WRfactor Rwork: 0.1563 / FOM work R set: 0.8393 / SU B: 7.109 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1332 / SU Rfree: 0.1311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 3640 4.8 %RANDOM
Rwork0.1637 71506 --
obs0.166 71506 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.41 Å2 / Biso mean: 31.657 Å2 / Biso min: 15.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0.18 Å2
2---0.21 Å20 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 1.9→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6752 0 12 543 7307
Biso mean--37.82 40.56 -
Num. residues----890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026950
X-RAY DIFFRACTIONr_bond_other_d0.0010.026118
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9359472
X-RAY DIFFRACTIONr_angle_other_deg0.934314144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81125.094318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.058151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4841526
X-RAY DIFFRACTIONr_chiral_restr0.130.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021606
X-RAY DIFFRACTIONr_mcbond_it2.0692.3993558
X-RAY DIFFRACTIONr_mcbond_other2.0672.3983557
X-RAY DIFFRACTIONr_mcangle_it2.8333.5864444
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 283 -
Rwork0.258 5225 -
all-5508 -
obs--96.01 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.26930.0062-0.00710.076-0.20390.70270.0014-0.04090.0165-0.0146-0.0391-0.0015-0.00450.08380.03760.04720.00770.01370.03060.00180.0459Chain A-30.87589.688324.0254
20.27480.1164-0.07830.0985-0.12090.74940.0097-0.0477-0.0042-0.02340.0232-0.0141-0.0076-0.061-0.03290.0281-0.01120.01740.07290.00010.0127Chain B-58.059131.67958.4755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 464
2X-RAY DIFFRACTION2B21 - 464

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