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- PDB-5amp: Geotrichum candidum Cel7A apo structure at 2.1A -

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Basic information

Entry
Database: PDB / ID: 5amp
TitleGeotrichum candidum Cel7A apo structure at 2.1A
ComponentsCELLOBIOHYDROLASE I
KeywordsHYDROLASE / CELLOBIOHYDROLASE
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region / metal ion binding
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 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. ...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 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Distorted Sandwich / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glucanase
Similarity search - Component
Biological speciesGALACTOMYCES CANDIDUM (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsBorisova, A.S. / Stahlberg, J.
CitationJournal: FEBS J. / Year: 2015
Title: Sequencing, Biochemical Characterization, Crystal Structure and Molecular Dynamics of Cellobiohydrolase Cel7A from Geotrichum Candidum 3C.
Authors: Borisova, A.S. / Eneyskaya, E.V. / Bobrov, K.S. / Jana, S. / Logachev, A. / Polev, D.E. / Lapidus, A.L. / Ibatullin, F.M. / Saleem, U. / Sandgren, M. / Payne, C.M. / Kulminskaya, A.A. / Stahlberg, J.
History
DepositionMar 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / 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 / _atom_site.label_entity_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 3.1Jan 10, 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 3.2Nov 6, 2024Group: Structure summary / Category: 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: CELLOBIOHYDROLASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7858
Polymers46,5211
Non-polymers1,2637
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.880, 90.560, 55.270
Angle α, β, γ (deg.)90.00, 109.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CELLOBIOHYDROLASE I / CELLOBIOHYDROLASE CEL7A


Mass: 46521.270 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 18-456 / Source method: isolated from a natural source / Source: (natural) GALACTOMYCES CANDIDUM (yeast) / Strain: 3C
References: UniProt: A0A088T0J9, cellulose 1,4-beta-cellobiosidase (reducing end)

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 2
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 , 3 types, 471 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.1 % / Description: NONE
Crystal growpH: 5.9
Details: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, 20% PEG 3350, pH 5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04088
DetectorType: CHESS / Detector: CCD / Date: Sep 26, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04088 Å / Relative weight: 1
ReflectionResolution: 2.03→51.98 Å / Num. obs: 24567 / % possible obs: 95.5 % / Observed criterion σ(I): 13.9 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9
Reflection shellResolution: 2.11→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.55 / % possible all: 75.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPI

1gpi


Resolution: 2.12→51.98 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.169 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19415 1125 5.1 %RANDOM
Rwork0.14614 ---
obs0.14863 20845 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.19 Å2
2--0.83 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.12→51.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 82 467 3808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023514
X-RAY DIFFRACTIONr_bond_other_d0.0010.023029
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.954815
X-RAY DIFFRACTIONr_angle_other_deg0.72736991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03725.935155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.94915494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.78158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02802
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4931.3291800
X-RAY DIFFRACTIONr_mcbond_other0.4931.3281799
X-RAY DIFFRACTIONr_mcangle_it0.9051.992265
X-RAY DIFFRACTIONr_mcangle_other0.9051.9922266
X-RAY DIFFRACTIONr_scbond_it0.4561.4051714
X-RAY DIFFRACTIONr_scbond_other0.4561.4051714
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7932.0822549
X-RAY DIFFRACTIONr_long_range_B_refined3.94411.794411
X-RAY DIFFRACTIONr_long_range_B_other3.45711.2544163
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.123→2.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 78 -
Rwork0.168 1366 -
obs--88.7 %

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