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- PDB-6ueh: Crystal structure of a ruminal GH26 endo-beta-1,4-mannanase -

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Basic information

Entry
Database: PDB / ID: 6ueh
TitleCrystal structure of a ruminal GH26 endo-beta-1,4-mannanase
ComponentsCow rumen GH26 endo-mannanase
KeywordsHYDROLASE / endo-mannanase / GH26 family / galactomannan / accessory domain
Function / homologyACETATE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.849 Å
AuthorsMandelli, F. / Morais, M.A.B. / Lima, E.A. / Persinoti, G.F. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015269820 and 2016199950 Brazil
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Spatially remote motifs cooperatively affect substrate preference of a ruminal GH26-type endo-beta-1,4-mannanase.
Authors: Mandelli, F. / de Morais, M.A.B. / de Lima, E.A. / Oliveira, L. / Persinoti, G.F. / Murakami, M.T.
History
DepositionSep 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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: Cow rumen GH26 endo-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4965
Polymers56,2791
Non-polymers2174
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.769, 53.748, 89.696
Angle α, β, γ (deg.)90.000, 103.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cow rumen GH26 endo-mannanase


Mass: 56279.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 8,000 (18% v/v), PEG 400 (10% v/v), 0.1M sodium acetate pH 5.5, 500 mM sodium chloride, Glycerol (10% v/v) and Dioxane (0.5% v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.849→43.607 Å / Num. obs: 43958 / % possible obs: 97.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.66 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.78
Reflection shellResolution: 1.849→1.91 Å / Num. unique obs: 4204 / CC1/2: 0.52

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.3refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZM8

3zm8


Resolution: 1.849→43.607 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.35
RfactorNum. reflection% reflection
Rfree0.2158 1997 4.54 %
Rwork0.1658 --
obs0.168 43951 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.25 Å2 / Biso mean: 23.34 Å2 / Biso min: 6.78 Å2
Refinement stepCycle: final / Resolution: 1.849→43.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 13 641 4606
Biso mean--42.23 32.27 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034076
X-RAY DIFFRACTIONf_angle_d0.7045535
X-RAY DIFFRACTIONf_chiral_restr0.028564
X-RAY DIFFRACTIONf_plane_restr0.003713
X-RAY DIFFRACTIONf_dihedral_angle_d12.221456
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.849-1.89510.31971380.2925287093
1.8951-1.94630.32681350.2588291695
1.9463-2.00360.32131440.2305292096
2.0036-2.06830.27211460.2188289896
2.0683-2.14220.2371250.2065300097
2.1422-2.22790.24651430.1782298497
2.2279-2.32930.23461460.1746296997
2.3293-2.45210.2191470.1732300598
2.4521-2.60580.21061510.1758301998
2.6058-2.80690.23851320.1706304398
2.8069-3.08930.21961460.1595303099
3.0893-3.53620.16851480.143307899
3.5362-4.45450.17751470.121307999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.92793.1478-2.23083.8088-3.09123.44880.0144-0.51591.11310.64770.34710.6705-1.134-0.9501-0.18120.37650.10750.01720.3193-0.08950.32311.3541.96955.975
29.62736.54510.55344.44940.37742.19350.2825-0.10550.42860.3044-0.10920.099-0.24980.0844-0.16110.19230.00510.00940.1714-0.03230.2053-2.54228.00457.468
34.5386-0.672-0.70177.13680.10624.6754-0.0119-0.3274-0.20170.41210.05480.16840.1238-0.03-0.02850.1306-0.02630.00550.16370.01960.1205-8.43715.05858.006
41.02761.1244-0.01694.4555-0.71411.1119-0.03090.05050.0104-0.13520.0322-0.050.03270.03750.00260.10910.0137-0.01540.1445-0.00540.1295-2.25125.15545.531
50.53860.0546-0.41610.19730.0960.48760.0544-0.03730.0294-0.0326-0.0081-0.0495-0.07480.1146-0.04580.1807-0.0014-0.01740.1778-0.00940.183219.25636.70723.335
61.40432.02661.96923.90744.25965.9295-0.1750.15570.1325-0.37170.03760.142-0.3520.23880.14210.19720.01640.00150.1720.03310.166823.19335.1522.501
72.50661.58051.29063.50742.75124.0504-0.04760.3651-0.0861-0.2266-0.07040.11050.0533-0.24930.08910.16310.0175-0.01260.2318-0.02060.181117.26425.6761.514
87.688-1.85630.76743.1593-0.63616.2981-0.05270.1114-0.0587-0.1883-0.08220.02820.1496-0.40330.11650.2055-0.05350.01080.1787-0.06320.161113.65615.6961.942
93.01680.7553-0.8472.0588-0.00792.0505-0.00510.0934-0.0852-0.004-0.0416-0.00920.14-0.09340.05170.14180.001-0.01390.1251-0.0140.111120.43722.07912.882
101.3024-0.3464-0.26371.73010.14330.83450.0149-0.0391-0.02840.0757-0.04260.05580.0334-0.07410.02580.1658-0.0283-0.00410.1893-0.01630.17229.18133.30624.917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 21:26 )A21 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:35 )A27 - 35
3X-RAY DIFFRACTION3( CHAIN A AND RESID 36:57 )A36 - 57
4X-RAY DIFFRACTION4( CHAIN A AND RESID 58:140 )A58 - 140
5X-RAY DIFFRACTION5( CHAIN A AND RESID 141:227 )A141 - 227
6X-RAY DIFFRACTION6( CHAIN A AND RESID 228:246 )A228 - 246
7X-RAY DIFFRACTION7( CHAIN A AND RESID 247:275 )A247 - 275
8X-RAY DIFFRACTION8( CHAIN A AND RESID 276:304 )A276 - 304
9X-RAY DIFFRACTION9( CHAIN A AND RESID 305:383 )A305 - 383
10X-RAY DIFFRACTION10( CHAIN A AND RESID 384:484 )A384 - 484

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