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- PDB-6y8f: An inactive (D136N and D137N) variant of alpha-1,6-mannanase, GH7... -

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Basic information

Entry
Database: PDB / ID: 6y8f
TitleAn inactive (D136N and D137N) variant of alpha-1,6-mannanase, GH76A of Salegentibacter sp. HEL1_6 in complex with alpha-1,6-mannotriose
ComponentsAlpha-1,6-endo-mannanase GH76A mutant
KeywordsHYDROLASE / Glycoside hydrolase / GH76 / Mannan / CAZymes / Mannanases
Biological speciesSalegentibacter sp. Hel_I_6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.472 Å
AuthorsHehemann, J.H. / Solanki, V.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) 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
DepositionMar 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: 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: Alpha-1,6-endo-mannanase GH76A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5015
Polymers43,8771
Non-polymers6254
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-10 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.311, 82.774, 49.700
Angle α, β, γ (deg.)90.000, 94.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-1,6-endo-mannanase GH76A mutant


Mass: 43876.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salegentibacter sp. Hel_I_6 (bacteria) / Plasmid: pET28a / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): BL21 DE3
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 14 % v/v 2-propanol, 30 % v/v Glycerol, 70 mM Sodium acetate pH 4.6, 140 mM Calcium chloride

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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 / Detector: PIXEL / Date: Dec 15, 2019
RadiationMonochromator: Si-111 and Si-113 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.47→82.77 Å / Num. obs: 50967 / % possible obs: 100 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.038 / Rrim(I) all: 0.091 / Net I/σ(I): 10.1 / Num. measured all: 287715 / Scaling rejects: 480
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
1.47-1.55.10.3711322525760.9280.1790.4133.3100
8.06-82.776.30.04720843330.9990.020.05121.399.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SHD

6shd


Resolution: 1.472→49.551 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.1994 2568 5.05 %
Rwork0.1624 --
obs0.1643 50884 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.25 Å2 / Biso mean: 19.9933 Å2 / Biso min: 7.32 Å2
Refinement stepCycle: final / Resolution: 1.472→49.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 37 452 3179
Biso mean--17.76 32.92 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032796
X-RAY DIFFRACTIONf_angle_d0.5573805
X-RAY DIFFRACTIONf_chiral_restr0.061408
X-RAY DIFFRACTIONf_plane_restr0.004493
X-RAY DIFFRACTIONf_dihedral_angle_d6.3991002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.472-1.50030.27881240.1982729
1.5003-1.53090.27621520.17942639
1.5309-1.56420.24311250.16892704
1.5642-1.60060.24371240.1812692
1.6006-1.64060.25261340.16772652
1.6406-1.6850.25071210.1552710
1.685-1.73460.21121320.14882656
1.7346-1.79060.21441710.15492681
1.7906-1.85460.20981450.15962684
1.8546-1.92880.21391550.16252657
1.9288-2.01660.21331350.16382696
2.0166-2.12290.19331680.15372638
2.1229-2.25590.19761490.15152668
2.2559-2.43010.18341500.1572689
2.4301-2.67470.17461730.16182671
2.6747-3.06160.18561530.17022673
3.0616-3.85710.18221360.15692712
3.8571-49.550.1911210.16772765

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