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- PDB-5jts: Structure of a beta-1,4-mannanase, SsGH134. -

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Basic information

Entry
Database: PDB / ID: 5jts
TitleStructure of a beta-1,4-mannanase, SsGH134.
Componentsbeta-1,4-mannanase
KeywordsHYDROLASE / beta-1 / 4-mannanase / carbohydrate degrading / glycosyl hydrolase
Function / homologymannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / Beta-1,4-mannanase
Function and homology information
Biological speciesStreptomyces sp. nrrl B-244 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsJin, Y. / Petricevic, M. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J.
Funding support United Kingdom, Australia, 2items
OrganizationGrant numberCountry
Eupropean Research CouncilAdG-322942 United Kingdom
Australian Research Council Australia
CitationJournal: ACS Cent Sci / Year: 2016
Title: A beta-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism.
Authors: Jin, Y. / Petricevic, M. / John, A. / Raich, L. / Jenkins, H. / Portela De Souza, L. / Cuskin, F. / Gilbert, H.J. / Rovira, C. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Oct 30, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.3May 1, 2024Group: 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: beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3796
Polymers18,0051
Non-polymers3745
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-8 kcal/mol
Surface area7050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.910, 53.680, 81.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein beta-1,4-mannanase


Mass: 18004.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Streptomyces sp. NRRL B-24484, Taxonomy ID: 1463833
Source: (gene. exp.) Streptomyces sp. nrrl B-244 (bacteria) / Strain: NRRL B-24484 / Plasmid: pHisMALP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus
References: UniProt: A0A1L1QK12*PLUS, mannan endo-1,4-beta-mannosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein stock in the buffer of 20 mM sodium phosphate, pH7.2, and 200 mM NaCl is mixed 1:1 with the precipitant consist of 20 % PEG6000, 0.15-0.2 M CaCl2,and 0.1 M Na HEPES, pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.09→33.62 Å / Num. obs: 68246 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 6.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.2
Reflection shellResolution: 1.09→1.12 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.532 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
ACORNphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpha-helical fragment

Resolution: 1.09→33.62 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.88 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16316 3439 5 %RANDOM
Rwork0.13913 ---
obs0.14039 64732 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.314 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20 Å2
2---0.48 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.09→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 23 150 1385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191289
X-RAY DIFFRACTIONr_bond_other_d0.0020.021158
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9331751
X-RAY DIFFRACTIONr_angle_other_deg1.03832663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30624.65558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55915186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.366156
X-RAY DIFFRACTIONr_chiral_restr0.1160.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021552
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02320
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_it1.3511.254673
X-RAY DIFFRACTIONr_mcbond_other1.3541.249672
X-RAY DIFFRACTIONr_mcangle_it1.7881.888843
X-RAY DIFFRACTIONr_mcangle_other1.7871.89844
X-RAY DIFFRACTIONr_scbond_it1.6391.413616
X-RAY DIFFRACTIONr_scbond_other1.6381.413616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9962.065902
X-RAY DIFFRACTIONr_long_range_B_refined3.01811.3491647
X-RAY DIFFRACTIONr_long_range_B_other3.01711.3561648
X-RAY DIFFRACTIONr_rigid_bond_restr2.07332447
X-RAY DIFFRACTIONr_sphericity_free25.882554
X-RAY DIFFRACTIONr_sphericity_bonded9.23652514
LS refinement shellResolution: 1.09→1.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 230 -
Rwork0.277 4762 -
obs--99.84 %

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