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Basic information

Entry
Database: PDB / ID: 2qha
TitleFrom Structure to Function: Insights into the Catalytic Substrate Specificity and Thermostability Displayed by Bacillus subtilis mannanase BCman
ComponentsBeta-1,4-mannanase
KeywordsHYDROLASE / Beta-barrel / His1-His23-Glu336 metal-binding motif / Disulfide bond / Shallow-dish-shaped active center
Function / homology
Function and homology information


substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / extracellular region / metal ion binding
Similarity search - Function
Mannan endo-1,4-beta-mannosidase B/E / 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
Mannan endo-1,4-beta-mannosidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.45 Å
AuthorsYan, X.X. / Liang, D.C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: From Structure to Function: Insights into the Catalytic Substrate Specificity and Thermostability Displayed by Bacillus subtilis Mannanase BCman
Authors: Yan, X.X. / An, X.M. / Gui, L.L. / Liang, D.C.
History
DepositionJul 1, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,4-mannanase
B: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5189
Polymers77,9262
Non-polymers5917
Water16,376909
1
A: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3055
Polymers38,9631
Non-polymers3424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2134
Polymers38,9631
Non-polymers2503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.179, 58.785, 63.463
Angle α, β, γ (deg.)83.03, 82.42, 77.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-1,4-mannanase / Beta-mannanase / BCman


Mass: 38963.156 Da / Num. of mol.: 2 / Fragment: UNP residues 27-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: Z-2 / Gene: MAN / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q5PSP8, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.12
Details: 7.5% PEG4000, 80mM sodium chloride, 100mM sodium citrate (pH5.12), VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→8 Å / Num. all: 95614 / Num. obs: 95614 / % possible obs: 90.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 51.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 11.3 / Num. unique all: 95614 / % possible all: 80.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.45→8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.033 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.098 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18993 5158 5.1 %RANDOM
Rwork0.15823 ---
obs0.15984 95614 90.84 %-
all-95614 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.881 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.03 Å20.01 Å2
2--0.04 Å2-0.02 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5392 0 32 909 6333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225580
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9287595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58124.571280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84715860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4911522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024366
X-RAY DIFFRACTIONr_nbd_refined0.20.22833
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2787
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.258
X-RAY DIFFRACTIONr_mcbond_it0.7291.53409
X-RAY DIFFRACTIONr_mcangle_it1.13325384
X-RAY DIFFRACTIONr_scbond_it2.12532541
X-RAY DIFFRACTIONr_scangle_it2.4574.52211
X-RAY DIFFRACTIONr_rigid_bond_restr2.08135950
X-RAY DIFFRACTIONr_sphericity_free2.6443911
X-RAY DIFFRACTIONr_sphericity_bonded1.99635423
LS refinement shellResolution: 1.45→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 364 -
Rwork0.237 6412 -
obs--85 %

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