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- PDB-4gwa: Crystal Structure of a GH7 Family Cellobiohydrolase from Limnoria... -

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Basic information

Entry
Database: PDB / ID: 4gwa
TitleCrystal Structure of a GH7 Family Cellobiohydrolase from Limnoria quadripunctata
ComponentsGH7 family protein
KeywordsHYDROLASE / cellobiohydrolase / Glycosyl hydrolase
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose catabolic process / extracellular region
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
Biological speciesLimnoria quadripunctata (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMcGeehan, J.E. / Martin, R.N.A. / Streeter, S.D. / Cragg, S.M. / Guille, M.J. / Schnorr, K.M. / Kern, M. / Bruce, N.C. / McQueen-Mason, S.J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance
Authors: Kern, M. / McGeehan, J.E. / Streeter, S.D. / Martin, R.N. / Besser, K. / Elias, L. / Eborall, W. / Malyon, G.P. / Payne, C.M. / Himmel, M.E. / Schnorr, K. / Beckham, G.T. / Cragg, S.M. / ...Authors: Kern, M. / McGeehan, J.E. / Streeter, S.D. / Martin, R.N. / Besser, K. / Elias, L. / Eborall, W. / Malyon, G.P. / Payne, C.M. / Himmel, M.E. / Schnorr, K. / Beckham, G.T. / Cragg, S.M. / Bruce, N.C. / McQueen-Mason, S.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes.
Authors: King, A.J. / Cragg, S.M. / Li, Y. / Dymond, J. / Guille, M.J. / Bowles, D.J. / Bruce, N.C. / Graham, I.A. / McQueen-Mason, S.J.
History
DepositionSep 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH7 family protein
B: GH7 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,26610
Polymers93,0722
Non-polymers1948
Water19,0241056
1
A: GH7 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6094
Polymers46,5361
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH7 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6576
Polymers46,5361
Non-polymers1225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.920, 54.050, 71.970
Angle α, β, γ (deg.)94.130, 95.700, 94.640
Int Tables number1
Space group name H-MP1

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Components

#1: Protein GH7 family protein


Mass: 46535.949 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limnoria quadripunctata (crustacean) / Gene: GH7B / Production host: Aspergillus oryzae (mold)
References: UniProt: D4HRL0, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1056 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 25% PEG 3350, 0.2M MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: PSI PILATUS 2M / Detector: PIXEL / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 100073 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 21.549 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.70.6640.4792.344917616918162850.58296.3
1.7-1.80.4180.3333.624591313486133750.39599.2
1.8-1.90.2960.2385.043672410699105970.28299
1.9-20.2150.1816.7229581873986110.21598.5
2-2.10.1650.1398.5523978705469010.16597.8
2.1-2.20.1320.1169.9219735587057420.13797.8
2.2-2.30.120.10311.1114983490647250.12396.3
2.3-2.40.1050.08711.8111925414239640.10695.7
2.4-2.50.0820.08314.0312584349634890.09799.8
2.5-2.90.0660.06816.7934282963895790.0899.4
2.9-30.0550.05919.696006168716780.06999.5
3-40.0380.04324.329780891687710.05198.4
4-50.0250.03129.579682316830250.03895.5
5-60.0250.03530.535376144114330.0499.4
6-80.0260.03829.524087110311000.04499.7
8-100.0250.03632.914503913900.04299.7
10-150.0220.03534.2411083013000.04199.7
15-300.0270.0434.593871251080.04786.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.35 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å14.84 Å
Translation2.7 Å14.84 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1712 / WRfactor Rwork: 0.1386 / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8974 / SU B: 1.578 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0833 / SU Rfree: 0.0854 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 4990 5 %RANDOM
Rwork0.148 ---
obs0.1498 100073 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.52 Å2 / Biso mean: 16.9712 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6514 0 8 1056 7578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.026727
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9299180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18925.791335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11115977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3281518
X-RAY DIFFRACTIONr_chiral_restr0.1350.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215350
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 379 -
Rwork0.218 6876 -
obs-16285 96.41 %

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