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- PDB-2a39: HUMICOLA INSOLENS ENDOCELLULASE EGI NATIVE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 2a39
TitleHUMICOLA INSOLENS ENDOCELLULASE EGI NATIVE STRUCTURE
ComponentsENDOGLUCANASE I
KeywordsENDOGLUCANASE / HYDROLASE / CELLULASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASE FAMILY 7 / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


cellulase / cellulase 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 speciesHumicola insolens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDavies, G.J. / Sulzenbacher, G. / Mackenzie, L. / Withers, S.G. / Divne, C. / Jones, T.A. / Woldike, H.F. / Schulein, M.
Citation
Journal: Biochem.J. / Year: 1998
Title: Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 A resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate.
Authors: MacKenzie, L.F. / Sulzenbacher, G. / Divne, C. / Jones, T.A. / Woldike, H.F. / Schulein, M. / Withers, S.G. / Davies, G.J.
#1: Journal: J.Biotechnol. / Year: 1997
Title: Oligosaccharide Specificity of a Family 7 Endoglucanase: Insertion of Potential Sugar-Binding Subsites
Authors: Davies, G.J. / Ducros, V. / Lewis, R.J. / Borchert, T.V. / Schulein, M.
History
DepositionJan 30, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Refinement description
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_struct_mod_residue / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 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_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.pdbx_dist_value / _struct_conn.pdbx_role / _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_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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: ENDOGLUCANASE I
B: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1086
Polymers88,2232
Non-polymers8854
Water7,566420
1
B: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5543
Polymers44,1121
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ENDOGLUCANASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5543
Polymers44,1121
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.900, 102.900, 282.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.79097, 0.40683, 0.45702), (0.38757, -0.24484, 0.88873), (0.47345, 0.88008, 0.03599)
Vector: -30.9723, 31.42876, -13.32844)

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Components

#1: Protein ENDOGLUCANASE I / CELLULASE / FAMILY 7 ENDOGLUCANASE


Mass: 44111.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PYROGLUTAMATE POST-TRANSLATIONAL MODIFICATION AT RESIDUE 1 N-LINKED N-ACETYLGLUCOSAMINE ON RESIDUE ASN 247
Source: (gene. exp.) Humicola insolens (fungus) / Gene: POTENTIAL / Production host: Aspergillus oryzae (mold) / References: UniProt: P56680, cellulase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 4.24 Å3/Da / Density % sol: 71 %
Description: MODEL FIRST SOLVED IN MONOCLINIC UNIT CELL AT LOW RESOLUTION. BAD REGIONS DELETED AND THEN THIS TRUNCATED CBH I MODEL USED TO SOLVE THIS TETRAGONAL FORM
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl11
2ammonium sulfate11

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 63790 / % possible obs: 96.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.209 / % possible all: 92.4
Reflection
*PLUS
Num. measured all: 289090
Reflection shell
*PLUS
% possible obs: 92.4 % / Mean I/σ(I) obs: 6

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Processing

Software
NameClassification
DENZOdata reduction
Agrovatadata reduction
AMoREphasing
REFMACrefinement
Agrovatadata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE TRICHODERMA REESEI CELLOBIOHYDROLASE PDB ENTRY 1CEL

1cel


Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: TWO MOLECULES IN THE ASYMMETRIC UNIT TIGHLY RESTRAINED
RfactorNum. reflection% reflectionSelection details
Rfree0.23 7592 10 %RANDOM
Rwork0.18 ---
obs-75122 96.6 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6176 0 56 420 6652
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.92
X-RAY DIFFRACTIONp_mcangle_it3.73
X-RAY DIFFRACTIONp_scbond_it3.92
X-RAY DIFFRACTIONp_scangle_it5.53
X-RAY DIFFRACTIONp_plane_restr0.0090.05
X-RAY DIFFRACTIONp_chiral_restr0.1220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1540.3
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor16.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.183 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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