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

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Basic information

Entry
Database: PDB / ID: 4haq
TitleCrystal Structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with cellobiose and cellotriose
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 / alpha-cellotriose / Exoglucanase GH7B
Similarity search - Component
Biological speciesLimnoria quadripunctata (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_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

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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)94,4889
Polymers93,0722
Non-polymers1,4167
Water10,160564
1
A: GH7 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0254
Polymers46,5361
Non-polymers4893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH7 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4635
Polymers46,5361
Non-polymers9274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.390, 54.270, 72.670
Angle α, β, γ (deg.)94.39, 96.33, 94.99
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Sugars , 2 types, 3 molecules

#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: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 568 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.19 Å3/Da / Density % sol: 43.83 % / Mosaicity: 0.64 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 0.2M MAGNESIUM CHLORIDE, 0.1M BIS-TRIS, 25% w/v PEG 3350, PH 8.0, VAPOUR DIFFUSION, SITTING 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: 1.9→45.04 Å / Num. obs: 59787 / % possible obs: 96 % / Redundancy: 3.4 % / Rsym value: 0.146 / Net I/σ(I): 6.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.513 / % possible all: 95.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.62 Å
Translation2.5 Å44.62 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: 1.9→44.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2062 / WRfactor Rwork: 0.1569 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8883 / SU B: 3.327 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1597 / SU Rfree: 0.1475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 3030 5.1 %RANDOM
Rwork0.1653 56752 --
obs0.168 59782 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.18 Å2 / Biso mean: 13.627 Å2 / Biso min: 3.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.01 Å2-0.01 Å2
2---0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6514 0 91 564 7169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026820
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.9469319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9075882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73825.808334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4215983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4071518
X-RAY DIFFRACTIONr_chiral_restr0.150.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215352
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 208 -
Rwork0.206 4218 -
all-4426 -
obs--95.53 %

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