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- PDB-1nlr: ENDO-1,4-BETA-GLUCANASE CELB2, CELLULASE, NATIVE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1nlr
TitleENDO-1,4-BETA-GLUCANASE CELB2, CELLULASE, NATIVE STRUCTURE
ComponentsENDO-1,4-BETA-GLUCANASE
KeywordsENDOGLUCANASE / GLYCOSYL HYDROLASE / FAMILY 12 / CELB2
Function / homology
Function and homology information


cellulase activity / polysaccharide binding / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / CBM2/CBM3, carbohydrate-binding domain superfamily ...Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / CBM2/CBM3, carbohydrate-binding domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.75 Å
AuthorsSulzenbacher, G. / Dupont, C. / Davies, G.J.
Citation
Journal: Biochemistry / Year: 1997
Title: The Streptomyces lividans family 12 endoglucanase: construction of the catalytic cre, expression, and X-ray structure at 1.75 A resolution.
Authors: Sulzenbacher, G. / Shareck, F. / Morosoli, R. / Dupont, C. / Davies, G.J.
#1: Journal: Nature / Year: 1997
Title: Erratum. Structure of the Inhibitory Receptor for Human Natural Killer Cells Resembles Haematopoietic Receptors
Authors: Fan, Q.R. / Mosyak, L. / Winter, C.C. / Wagtmann, N. / Long, E.O. / Wiley, D.C.
#2: Journal: Appl.Environ.Microbiol. / Year: 1994
Title: Purification and Characterization of the Celb Endoglucanase from Streptomyces Lividans 66 and DNA Sequence of the Encoding Gene
Authors: Wittmann, S. / Shareck, F. / Kluepfel, D. / Morosoli, R.
History
DepositionOct 27, 1997Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: ENDO-1,4-BETA-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)24,5951
Polymers24,5951
Non-polymers00
Water3,603200
1
A: ENDO-1,4-BETA-GLUCANASE

A: ENDO-1,4-BETA-GLUCANASE


Theoretical massNumber of molelcules
Total (without water)49,1892
Polymers49,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)48.492, 95.479, 40.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ENDO-1,4-BETA-GLUCANASE / CELB / CELB2


Mass: 24594.713 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Fragment: CATALYTIC DOMAIN / Production host: Streptomyces lividans (bacteria) / Strain (production host): 66 / References: UniProt: Q54331, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE COORDINATES GIVEN DEFINE THE STRUCTURE OF CELB2, THE TRUNCATED, CATALYTICALLY COMPETENT, FORM ...THE COORDINATES GIVEN DEFINE THE STRUCTURE OF CELB2, THE TRUNCATED, CATALYTICALLY COMPETENT, FORM OF ENDOGLUCANASE CELB. CELB CONSISTS OF A C-TERMINAL CATALYTIC DOMAIN, A FLEXIBLE LINKER REGION AND A N-TERMINAL CELLULOSE-BINDING-DOMAIN. ENDOGLUCANASE CELB BELONGS TO GLYCOSYL HYDROLASE FAMILY 12. THE ENZYME PERFORMS CATALYSIS WITH RETENTION OF CONFIGURATION AT THE ANOMERIC CARBON. THE CATALYTIC NUCLEOPHILE IS GLU 120 AND THE GENERAL ACID/ BASE IS GLU 203.
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: 2.01 Å3/Da / Density % sol: 38.2 %
Crystal growMethod: vapor diffusion / pH: 4.5
Details: 30 % PEG 1500, PH 4.5 FOR ACETATE BUFFER METHOD: HANGING DROP VAPOUR DIFFUSION, vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlenzyme1drop
330 %(w/w)PEG15001reservoir
2acetate1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 17, 1997 / Details: FOCUSING MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→15 Å / Num. obs: 18747 / % possible obs: 95.6 % / Redundancy: 6.98 % / Biso Wilson estimate: 18.51 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 31.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.21 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 5.96 / % possible all: 68.5
Reflection
*PLUS
% possible obs: 93.7 % / Redundancy: 6.77 %
Reflection shell
*PLUS
Lowest resolution: 1.84 Å / % possible obs: 67.9 % / Redundancy: 2.78 % / Rmerge(I) obs: 0.287

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.75→15 Å / Cross valid method: FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.24 978 5 %RANDOM
Rwork0.187 ---
obs-17769 95.6 %-
Displacement parametersBiso mean: 20.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1655 0 9 200 1864
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1573
X-RAY DIFFRACTIONp_mcangle_it2.9274
X-RAY DIFFRACTIONp_scbond_it3.3844.5
X-RAY DIFFRACTIONp_scangle_it4.2275.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1390.15
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1770.3
X-RAY DIFFRACTIONp_planar_tor4.56
X-RAY DIFFRACTIONp_staggered_tor14.715
X-RAY DIFFRACTIONp_orthonormal_tor27.830
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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