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- PDB-2nlr: STREPTOMYCES LIVIDANS ENDOGLUCANASE (EC: 3.2.1.4) COMPLEX WITH MO... -

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Basic information

Entry
Database: PDB / ID: 2nlr
TitleSTREPTOMYCES LIVIDANS ENDOGLUCANASE (EC: 3.2.1.4) COMPLEX WITH MODIFIED GLUCOSE TRIMER
ComponentsPROTEIN (ENDOGLUCANASE (E.C.3.2.1.4))
KeywordsHYDROLASE / HYDROLASE (ENDOGLUCANASE) / GLYCOSYL HYDROLASE / FAMILY 12 / ENDOGLUCANASE / CELB2 / GLYCOSYL-ENZYME INTERMEDIATE
Function / homology
Function and homology information


polysaccharide binding / cellulase activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSulzenbacher, G. / Dupont, C. / Davies, G.J.
Citation
Journal: Biochemistry / Year: 1999
Title: The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution.
Authors: Sulzenbacher, G. / Mackenzie, L.F. / Wilson, K.S. / Withers, S.G. / Dupont, C. / Davies, G.J.
#1: Journal: Biochemistry / Year: 1997
Title: The Streptomyces lividans Family 12 Endoglucanase: Construction of the Catalytic Core, Expression and X-Ray Structure at 1.75 A Resolution
Authors: Sulzenbacher, G. / Sharek, F. / Morosoli, R. / Dupont, C. / Davies, G.J.
#2: Journal: Appl.Environ.Microbiol. / Year: 1994
Title: Purification and Characterisation 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
DepositionNov 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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: PROTEIN (ENDOGLUCANASE (E.C.3.2.1.4))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0852
Polymers24,5791
Non-polymers5061
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.960, 65.960, 88.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1218-

HOH

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Components

#1: Protein PROTEIN (ENDOGLUCANASE (E.C.3.2.1.4)) / CELB


Mass: 24578.713 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Strain: 66 / Gene: CELB / Plasmid: PIAF9, PIAF18 / Production host: Streptomyces lividans (bacteria) / Strain (production host): 66
References: GenBank: 2462718, UniProt: Q54331*PLUS, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-beta-D-glucopyranose


Type: oligosaccharide / Mass: 506.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*F][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp2fluoro]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDOGLUCANASE CELB BELONGS TO GLYCOSYL HYDROLASASE FAMILY 12. THE ENZYME PERFORMS CATALYSIS WITH ...ENDOGLUCANASE CELB BELONGS TO GLYCOSYL HYDROLASASE FAMILY 12. THE ENZYME PERFORMS CATALYSIS WITH RETENTION OF CONFIGURATION AT THE ANOMERIC CARBON. THE COORDINATES GIVEN DEFINE THE STRUCTURE OF CELB2, THE TRUNCATED, CATALYTICALLY COMPETENT, FORM OF ENDOGLUCANASE CELB, IN COMPLEX WITH 2-DEOXY-2-FLUORO-CELLOTRIOSE. TWO SPECIES ARE PRESENT IN THE CRYSTAL, ONE IS THE GLYCOSYL-ENZYME INTERMEDIATE, WITH 2-DEOXY-2-FLUORO- CELLOTRIOSYL COVALENTLY BOUND TO THE NUCLEOPHILE GLU 120, THE OTHER SPECIES IS THE REACTION PRODUCT 2-DEOXY-2-FLUORO-CELLOTRIOSE BOUND TO THE ACTIVE SITE. THIS IS REPRESENTED BY A DOUBLE CONFORMATION FOR THE PROXIMAL SACCHARIDE, 2-DEOXY-2FLUORO-GLUCOSE.
Sequence detailsTHE CONSTRUCT CELB2 WAS AMPLIFIED UP TO RESIDUE 274 (U04629 WHICH IS THE END OF THE JUNCTION ...THE CONSTRUCT CELB2 WAS AMPLIFIED UP TO RESIDUE 274 (U04629 WHICH IS THE END OF THE JUNCTION BETWEEN THE CATALYTIC DOMAIN AND THE CELLULOSE BINDING DOMAIN OF CELB. THE DEPOSITED COORDINATES CORRESPOND TO THE MATURE CATALYTIC DOMAIN OF CELB. RESIDUES 1 TO 40 OF THE ENTRY U04629 CORRESPOND TO THE SIGNALLING PEPTIDE OF CELB AND ARE NOT PART OF THE MATURE PROTEIN CELB2. IT FOLLOWS THAT THERE IS A DISCREPANCY BETWEEN THE NUMBERING OF THE ENTRY U04629 AND THE PESENT ENTRY, CORRESPONDING TO THE 40 MISSING RESIDUES OF THE C-TERMINAL. RESIDUES 263 TO 274 (U04629) CORRESPOND TO THE FLEXIBLE LINKER REGION, NOT VISIBLE IN THE ELECTRON DENSITY MAP, MAY BE NOT EVEN PRESENT IN THE PROTEIN BECAUSE OF PROTEOLYTIC DIGESTION. RESIDUES 274 -381 ((U04629) CORRESPOND TO THE CELLULOSE BINDING DOMAIN (CBD-DOMAIN) AND ARE NOT PRESENT IN THIS ENTRY. CELB (ENTRY U04629) CELB2 (PRESENT ENTRY) RESIDUE 1-40 (SIGNALLING PEP.) ABSENT RESIDUE 41-263 (CATALYTIC DOM.) RESIDUE 1-222 RESIDUE 263-274 (FLEXIBLE LINKER) ABSENT (RES. 223-234) RESIDUE 274-381 ( CBD-DOMAIN) ABSENT

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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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 4.5 / Details: pH 4.5
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.2→25 Å / Num. obs: 69645 / % possible obs: 99.1 % / Redundancy: 5.96 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.93
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 4.49 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3.74 / % possible all: 97.2
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NLR

1nlr


Resolution: 1.2→25 Å / Num. parameters: 20212 / Num. restraintsaints: 28536 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: TARGET VALUES FOR 2-DEOXY-2-FLUORO-CELLOTRIO WERE TAKEN FROM THE CRYSTAL STRUCTURE OF METHYL-BETA-CELL TRIOSIDE; S.RAYMOND, B.HENRISSAT,D.T.QUI,A.KVICK, H.CHANZY, ...StereochEM target val spec case: TARGET VALUES FOR 2-DEOXY-2-FLUORO-CELLOTRIO WERE TAKEN FROM THE CRYSTAL STRUCTURE OF METHYL-BETA-CELL TRIOSIDE; S.RAYMOND, B.HENRISSAT,D.T.QUI,A.KVICK, H.CHANZY, CAROBOHYDRATE RESEARCH 277,209-229.
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.95. RESIDUES ASP 104, GLU 120 AND MET 122 EXHIBIT DISORDER WHICH IS COUPLED TO THE TWO CONFORMATIONS OF 2-DEOXY-2-FLUORO-GLUCOSE. THE ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.95. RESIDUES ASP 104, GLU 120 AND MET 122 EXHIBIT DISORDER WHICH IS COUPLED TO THE TWO CONFORMATIONS OF 2-DEOXY-2-FLUORO-GLUCOSE. THE NUCLEOPHILE GLU 120 IS PRESENT IN TRIPLE CONFORMATION. CONFORMER B AND C ARE COVALENTLY LINKED TO THE FLUOROCELLOTRIOSIDE. HYDROGEN ATOMS HAVE NOT BEEN LOCATED ONLY ON ALL DISORDERED RESIDUES. ASP 95 AND GLY 96 SIT NEAR THE CRYSTALLOGRAPHIC TWOFOLD AXIS AND ARE PRESENT IN TWO ALTERNATIVE AND COMPLEMENTARY CONFORMATIONS. THR 222 IS THE LAST VISIBLE RESIDUE IN THE ELECTRON DENSITY MAP. PRO 76 IS PRESENT IN THE CIS CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1423 3513 5 %RANDOM
all0.1119 69645 --
obs0.1112 -99.1 %-
Solvent computationSolvent model: SHELX SWAT
Refine analyzeNum. disordered residues: 34 / Occupancy sum hydrogen: 1509 / Occupancy sum non hydrogen: 1936.6
Refinement stepCycle: LAST / Resolution: 1.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 45 270 1977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0.002
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.025
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.084
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.032
X-RAY DIFFRACTIONs_chiral_restr0.082

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