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- PDB-7dvj: Structure of beta-mannanase BaMan113A with mannobiose -

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Basic information

Entry
Database: PDB / ID: 7dvj
TitleStructure of beta-mannanase BaMan113A with mannobiose
ComponentsEndo-beta-1,4-mannanase
KeywordsHYDROLASE / Complex
Function / homologyGlycoside hydrolase superfamily / 4beta-beta-mannobiose / Endo-beta-1,4-mannanase
Function and homology information
Biological speciesBacillus sp. N16-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLiu, W.T. / Liu, W.D. / Zheng, Y.Y.
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Functional and structural investigation of a novel beta-mannanase BaMan113A from Bacillus sp. N16-5.
Authors: Liu, W. / Ma, C. / Liu, W. / Zheng, Y. / Chen, C.C. / Liang, A. / Luo, X. / Li, Z. / Ma, W. / Song, Y. / Guo, R.T. / Zhang, T.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,8644
Polymers81,1792
Non-polymers6852
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint1 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.493, 110.284, 150.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Endo-beta-1,4-mannanase / BaMan113B


Mass: 40589.691 Da / Num. of mol.: 2 / Mutation: E142A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. N16-5 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140EH91
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-mannobiose
DescriptorTypeProgram
DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 108815 / % possible obs: 97.9 % / Redundancy: 7.4 % / CC1/2: 0.858 / Net I/σ(I): 11.8
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 10962 / CC1/2: 0.905

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CIV

3civ


Resolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.827 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 5413 5 %RANDOM
Rwork0.1654 ---
obs0.1665 103293 96.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.35 Å2 / Biso mean: 21.568 Å2 / Biso min: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å2-0 Å20 Å2
2--3.1 Å2-0 Å2
3----1.39 Å2
Refinement stepCycle: final / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 46 764 6053
Biso mean--24.43 35.41 -
Num. residues----633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135462
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184737
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6497403
X-RAY DIFFRACTIONr_angle_other_deg1.5141.58911028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4725631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44122.765311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6715908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4951529
X-RAY DIFFRACTIONr_chiral_restr0.1160.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026068
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021259
LS refinement shellResolution: 1.654→1.697 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 317 -
Rwork0.308 6092 -
all-6409 -
obs--77.92 %

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