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- PDB-4hap: Crystal Structure of a GH7 family cellobiohydrolase from Limnoria... -

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Basic information

Entry
Database: PDB / ID: 4hap
TitleCrystal Structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with cellobiose
ComponentsGH7 family protein
KeywordsHYDROLASE / cellobiohydrolase
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
beta-cellobiose / Exoglucanase GH7B
Similarity search - Component
Biological speciesLimnoria quadripunctata (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMartin, R.N.A. / McGeehan, J.E. / 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 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 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
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / 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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Oct 30, 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: GH7 family protein
B: GH7 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,07910
Polymers93,0722
Non-polymers1,0078
Water22,7171261
1
A: GH7 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1617
Polymers46,5361
Non-polymers6256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH7 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9183
Polymers46,5361
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.260, 54.190, 72.450
Angle α, β, γ (deg.)94.260, 96.020, 94.990
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: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1261 / 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: 2.18 Å3/Da / Density % sol: 43.48 % / Mosaicity: 1.15 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Sodium Acetate, 15% w/v PEG 6000, 0.5M CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2012
RadiationMonochromator: Si(111)Dual Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.6→71.795 Å / Num. all: 96748 / Num. obs: 96748 / % possible obs: 93.4 % / Redundancy: 3.3 % / Rsym value: 0.113 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.693.10.7210.5951.242611138910.40.7210.5952.291.9
1.69-1.793.30.4870.4081.743321131970.2630.4870.4083.292.4
1.79-1.913.40.3320.2792.442682125580.1770.3320.2794.592.9
1.91-2.073.20.2170.182.837489116770.1190.2170.186.293.2
2.07-2.263.20.1530.1275.234300107870.0850.1530.127893.8
2.26-2.533.50.1210.1026.83415098060.0640.1210.1029.894.3
2.53-2.923.20.1020.08482777886650.0560.1020.08411.294.3
2.92-3.583.20.0790.0669.42364973210.0430.0790.06614.294.5
3.58-5.063.40.070.05910.41947656550.0370.070.05917.194.5
5.06-39.9053.40.0740.0629.31069831910.040.0740.06215.597

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.9 Å
Translation2.5 Å39.9 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GWA

4gwa


Resolution: 1.6→39.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1896 / WRfactor Rwork: 0.1436 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9038 / SU B: 1.611 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0872 / SU Rfree: 0.0932 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 4846 5 %RANDOM
Rwork0.1444 ---
obs0.1467 96745 93.43 %-
all-98248 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.59 Å2 / Biso mean: 14.5747 Å2 / Biso min: 3.93 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6514 0 59 1261 7834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.026844
X-RAY DIFFRACTIONr_bond_other_d0.0020.025822
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.9429361
X-RAY DIFFRACTIONr_angle_other_deg0.9453.00513499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34825.833336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.388151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0121518
X-RAY DIFFRACTIONr_chiral_restr0.1290.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021546
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 333 -
Rwork0.246 6693 -
all-7026 -
obs--91.64 %

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