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- PDB-4cd4: The structure of GH26 beta-mannanase CjMan26C from Cellvibrio jap... -

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Basic information

Entry
Database: PDB / ID: 4cd4
TitleThe structure of GH26 beta-mannanase CjMan26C from Cellvibrio japonicus in complex with ManIFG
ComponentsENDO-1,4-BETA MANNANASE, PUTATIVE, MAN26C
KeywordsHYDROLASE / BETA-MANNOSIDASE / MANNOSIDASE / GLYCOSIDE HYDROLASE / GH26 / GH113 / CAZY / ENZYME-CARBOHYDRATE INTERACTION / MANNOSE / GLYCOSIDASE INHIBITION / QUANTUM MECHANICS / BIOCATALYSIS / CONFORMATION
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity
Similarity search - Function
Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Endo-1, 4-beta mannanase, putative, man26C
Similarity search - Component
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWilliams, R.J. / Iglesias-Fernandez, J. / Stepper, J. / Jackson, A. / Thompson, A.J. / Lowe, E.C. / White, J.M. / Gilbert, H.J. / Rovira, C. / Davies, G.J. / Williams, S.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate.
Authors: Williams, R.J. / Iglesias-Fernandez, J. / Stepper, J. / Jackson, A. / Thompson, A.J. / Lowe, E.C. / White, J.M. / Gilbert, H.J. / Rovira, C. / Davies, G.J. / Williams, S.J.
History
DepositionOct 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Non-polymer description
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 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: ENDO-1,4-BETA MANNANASE, PUTATIVE, MAN26C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9805
Polymers46,6071
Non-polymers3734
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.518, 84.518, 244.491
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ENDO-1,4-BETA MANNANASE, PUTATIVE, MAN26C / CJMAN26C BETA-MANNANASE


Mass: 46606.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: UEDA107 / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: B3PGI1, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL / Afegostat


Mass: 147.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 5.6 / Details: 100 MM SODIUM CITRATE PH 5.6, 15% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→54.46 Å / Num. obs: 142150 / % possible obs: 88.8 % / Observed criterion σ(I): 2 / Redundancy: 14.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.9
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 0.8 / % possible all: 20.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
xia2IMPLEMENTATION OF XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VX7

2vx7


Resolution: 1.2→73.19 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.85 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.13385 7145 5 %RANDOM
Rwork0.11129 ---
obs0.11241 134854 88.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.2→73.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 23 746 3702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193179
X-RAY DIFFRACTIONr_bond_other_d0.0010.022919
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9334357
X-RAY DIFFRACTIONr_angle_other_deg1.28536706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12723.373166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23715491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1141524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023701
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02815
X-RAY DIFFRACTIONr_nbd_refined0.2720.21612
X-RAY DIFFRACTIONr_nbd_other0.1960.22649
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21541
X-RAY DIFFRACTIONr_nbtor_other0.0790.21580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3790.296
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.991.0921510
X-RAY DIFFRACTIONr_mcbond_other0.9891.0911511
X-RAY DIFFRACTIONr_mcangle_it1.2281.6461897
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.511.2911669
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7681.8562441
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.39136098
X-RAY DIFFRACTIONr_sphericity_free34.1595150
X-RAY DIFFRACTIONr_sphericity_bonded8.37156600
LS refinement shellResolution: 1.202→1.234 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 148 -
Rwork0.379 3119 -
obs--28.11 %

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