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- PDB-3eii: Zinc-bound glycoside hydrolase 61 E from Thielavia terrestris -

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Basic information

Entry
Database: PDB / ID: 3eii
TitleZinc-bound glycoside hydrolase 61 E from Thielavia terrestris
Componentsprotein GH61E
KeywordsUNKNOWN FUNCTION / beta sandwich / metal binding site / fibronectin type III
Function / homology
Function and homology information


cellulase / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61) / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesThielavia terrestris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsSalbo, R. / Welner, D. / Lo Leggio, L. / Harris, P. / McFarland, K.
CitationJournal: Biochemistry / Year: 2010
Title: Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family.
Authors: Harris, P.V. / Welner, D. / McFarland, K.C. / Re, E. / Navarro Poulsen, J.C. / Brown, K. / Salbo, R. / Ding, H. / Vlasenko, E. / Merino, S. / Xu, F. / Cherry, J. / Larsen, S. / Lo Leggio, L.
History
DepositionSep 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein GH61E
B: protein GH61E
C: protein GH61E
D: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,79827
Polymers90,2804
Non-polymers2,51823
Water12,538696
1
A: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1456
Polymers22,5701
Non-polymers5755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3068
Polymers22,5701
Non-polymers7367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2067
Polymers22,5701
Non-polymers6366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: protein GH61E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1416
Polymers22,5701
Non-polymers5715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)220.918, 220.918, 220.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
protein GH61E


Mass: 22569.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thielavia terrestris (fungus) / Strain: NRLL 8126 / Gene: gh61e / Plasmid: pAlLo28 / Production host: Aspergillus oryzae (mold) / Strain (production host): JaL250 / References: UniProt: D0VWZ9*PLUS
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 715 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE IS REFERENCED AS ENTRY GENESEQP:AEB90523

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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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M MgSO4, 0.1 M MES, soaked for a few minutes in 1.8 M ZnSO4, 0.1M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 42338 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 27.2 Å2 / Rsym value: 0.109 / Net I/σ(I): 9.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.333 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAXLABPROGRAMdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Magnesium-bound glycoside hydrolase 61 E from Thielavia terrestris (deposition in progress)

Resolution: 2.25→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.0E-5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 2117 -random
Rwork0.2171 ---
obs-42338 93.2 %-
Displacement parametersBiso mean: 20.3 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6396 0 129 696 7221
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.010436
X-RAY DIFFRACTIONc_angle_deg1.48059
X-RAY DIFFRACTIONc_mcbond_it1.1051.5
X-RAY DIFFRACTIONc_mcangle_it1.7692
X-RAY DIFFRACTIONc_scbond_it1.6752
X-RAY DIFFRACTIONc_scangle_it2.3962.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.25-2.350.22433850.1923X-RAY DIFFRACTION7807
2.35-2.480.24934610.2089X-RAY DIFFRACTION9171
2.48-2.630.2565060.2138X-RAY DIFFRACTION9597
2.63-2.830.28694820.2391X-RAY DIFFRACTION9983
2.83-3.120.27215730.2398X-RAY DIFFRACTION10201
3.12-3.570.32614650.3069X-RAY DIFFRACTION10213

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