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- PDB-1uu5: X-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMICOLA GRISE... -

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Basic information

Entry
Database: PDB / ID: 1uu5
TitleX-RAY CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMICOLA GRISEA CEL12A SOAKED WITH CELLOTETRAOSE
ComponentsENDO-BETA-1,4-GLUCANASE
KeywordsHYDROLASE / CELLULASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSYL HYDROLASE / GH FAMILY 12 / HUMICOLA GRISEA CEL12A / LIGAND COMPLEX
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Endoglucanase
Similarity search - Component
Biological speciesHUMICOLA GRISEA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.67 Å
AuthorsBerglund, G.I. / Shaw, A. / Stahlberg, J. / Kenne, L. / Driguez, T.H. / Mitchinson, C. / Sandgren, M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Complex Structures Reveal How Substrate is Bound in the -4 to the +2 Binding Sites of Humicola Grisea Cel12A
Authors: Sandgren, M. / Berglund, G.I. / Shaw, A. / Stahlberg, J. / Kenne, L. / Desmet, T. / Mitchinson, C.
History
DepositionDec 15, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-BETA-1,4-GLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6143
Polymers25,8891
Non-polymers7262
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.501, 49.501, 167.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ENDO-BETA-1,4-GLUCANASE / ENDOGLUCANASE / CEL12A


Mass: 25888.586 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 31-254
Source method: isolated from a genetically manipulated source
Details: THE CRYSTAL STRUCTURE REPRESENTS A COMPLEX WITH A MIXED BETA-1,3-1,4-GLUCAN. THE BETA-1,3 LINKAGE IS LOCATED BETWEEN THE TWO CELLOBIOSE UNITS IN THE TETRAOSE LIGAND INDICATING A ...Details: THE CRYSTAL STRUCTURE REPRESENTS A COMPLEX WITH A MIXED BETA-1,3-1,4-GLUCAN. THE BETA-1,3 LINKAGE IS LOCATED BETWEEN THE TWO CELLOBIOSE UNITS IN THE TETRAOSE LIGAND INDICATING A TRANSGLYCOSYLATION REACTION TAKING PLACE IN THE SOAKING EXPERIMENT
Source: (gene. exp.) HUMICOLA GRISEA (fungus) / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: Q8NJY3, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b3-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.8 Å3/Da / Density % sol: 31.7 %
Description: INITIAL MODEL WAS PRODUCED BY RIGID BODY REFINEMENT USING THE APO PROTEIN STRUCTURE PDB ENTRY 1OLR
Crystal growpH: 3.1
Details: CRYSTALS GREW FROM A PROTEIN STOCK SOLUTION CONTAINING 1MG/ML PROTEIN IN 0.05 M BIS TRIS PROPANE AND 0.05 M AMMONIUM ACETATE, PH 8 CRYSTALS WERE CRYOPROTECTED IN UNBUFFERED 50% MME PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.671→47.673 Å / Num. obs: 24865 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 25.8
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 4.8 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.67→47.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH OCCUPANCY OF 0.00 FOR WHICH THE B-FACTORS HAVE BEEN REFINED. ATOMS ARE ASSIGNED REDUCED OCCUPANCIES WHEN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH OCCUPANCY OF 0.00 FOR WHICH THE B-FACTORS HAVE BEEN REFINED. ATOMS ARE ASSIGNED REDUCED OCCUPANCIES WHEN ELECTRON DENSITY IS WEAK OR ATOMS HAVE PARTIAL OCCUPANCY. THE FOLLOWING RESIDUES HAVE BEEN MODELLED WITH MULTIPLE CONFORMATIONS: A6, A146 AND A213 ALSO WATERS Z23, Z35, Z45, Z73
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1030 4.1 %RANDOM
Rwork0.162 ---
obs0.164 23833 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.67→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 49 178 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211946
X-RAY DIFFRACTIONr_bond_other_d00.021612
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9382659
X-RAY DIFFRACTIONr_angle_other_deg3.75733725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022182
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02447
X-RAY DIFFRACTIONr_nbd_refined0.1790.2286
X-RAY DIFFRACTIONr_nbd_other0.2760.21851
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1130.2926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7181.51118
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37621793
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9853828
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0074.5863
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.236 69
Rwork0.169 1698

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