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- PDB-6shm: An inactive (D136A and D137A) variant of alpha-1,6-mannanase, GH7... -

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Basic information

Entry
Database: PDB / ID: 6shm
TitleAn inactive (D136A and D137A) variant of alpha-1,6-mannanase, GH76A of Salegentibacter sp. HEL1_6 in complex with alpha-1,6-mannotetrose
ComponentsMutant alpha-1,6-mannanase GH76A
KeywordsHYDROLASE / Glycoside hydrolase / Mannanase / mannotetrose / GH76 / CAZyme / polysaccharide
Biological speciesSalegentibacter sp. Hel_I_6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHehemann, J.H. / Solanki, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Isme J / Year: 2022
Title: Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi.
Authors: Solanki, V. / Kruger, K. / Crawford, C.J. / Pardo-Vargas, A. / Danglad-Flores, J. / Hoang, K.L.M. / Klassen, L. / Abbott, D.W. / Seeberger, P.H. / Amann, R.I. / Teeling, H. / Hehemann, J.H.
History
DepositionAug 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mutant alpha-1,6-mannanase GH76A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7454
Polymers43,7911
Non-polymers9543
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint16 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.150, 85.310, 95.030
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 Mutant alpha-1,6-mannanase GH76A


Mass: 43790.688 Da / Num. of mol.: 1 / Mutation: D136A and D137A
Source method: isolated from a genetically manipulated source
Details: WP_051935954.1 / Source: (gene. exp.) Salegentibacter sp. Hel_I_6 (bacteria) / Gene: GH76A / Plasmid: pET28a / Production host: Escherichia coli K-12 (bacteria)
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122h-1a_1-5]/1-1-1-1/a6-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.6 M Tri-sodium citrate 10 % Glycerol 0.1 M MES monohydrate pH 6.5
PH range: 6-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→63.48 Å / Num. obs: 24400 / % possible obs: 99.2 % / Redundancy: 9.3 % / CC1/2: 0.279 / Rmerge(I) obs: 5.441 / Rpim(I) all: 2.333 / Rrim(I) all: 0.5969 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9470.136021069415220.2416.23615.103197.8
9.11-47.5110.10.09628262800.9790.0320.10122.499.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SHD

6shd


Resolution: 1.9→47.51 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.527 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 1271 5.2 %RANDOM
Rwork0.1181 ---
obs0.1208 23304 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.61 Å2 / Biso mean: 12.801 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 63 351 3103
Biso mean--21.08 27.32 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132819
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172448
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.6533829
X-RAY DIFFRACTIONr_angle_other_deg1.661.5965707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08324.967153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24115441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.576158
X-RAY DIFFRACTIONr_chiral_restr0.090.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02571
X-RAY DIFFRACTIONr_rigid_bond_restr3.1235266
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 90 -
Rwork0.15 1697 -
all-1787 -
obs--99.94 %

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