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- PDB-7dvz: Structure of a novel beta-mannanase BaMan113A from Bacillus sp. N... -

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Basic information

Entry
Database: PDB / ID: 7dvz
TitleStructure of a novel beta-mannanase BaMan113A from Bacillus sp. N16-5, N236Y mutation.
ComponentsEndo-beta-1,4-mannanase
KeywordsHYDROLASE / Complex
Function / homology: / Glycoside Hydrolase Family 113 / Glycoside hydrolase superfamily / Endo-beta-1,4-mannanase
Function and homology information
Biological speciesBacillus sp. N16-5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, W.T. / Liu, W.D. / Zheng, Y.Y.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Functional and structural investigation of a Novel beta-Mannanase BaMan113B from Bacillus sp. N16-5
Authors: Liu, W.T. / Liu, W.D. / Zheng, Y.Y.
History
DepositionJan 15, 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


Theoretical massNumber of molelcules
Total (without water)81,2782
Polymers81,2782
Non-polymers00
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-13 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.936, 150.634, 108.648
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: 40638.762 Da / Num. of mol.: 2 / Mutation: E142A, N236Y
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
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 PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 62836 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.955 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 6171 / CC1/2: 0.971

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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: 3ICV

3icv


Resolution: 2→24.88 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.704 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1726 3147 5 %RANDOM
Rwork0.1407 ---
obs0.1423 59587 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.73 Å2 / Biso mean: 21.27 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å2-0 Å2
2---0.99 Å20 Å2
3---1.28 Å2
Refinement stepCycle: final / Resolution: 2→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5303 0 0 618 5921
Biso mean---34.36 -
Num. residues----640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135477
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184795
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6377415
X-RAY DIFFRACTIONr_angle_other_deg1.431.57811142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4015639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05322.556313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64415924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9111531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021281
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 217 -
Rwork0.175 4257 -
all-4474 -
obs--98.94 %

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