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- PDB-6mpc: Crystal structure of E257A mutant of BlMan5B -

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Basic information

Entry
Database: PDB / ID: 6mpc
TitleCrystal structure of E257A mutant of BlMan5B
ComponentsBlMan5B
KeywordsHYDROLASE / Family GH5 / subfamily 18 / beta-mannosidase
Function / homologyGlycoside hydrolase superfamily / Glycosyl hydrolase
Function and homology information
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLorizolla-Cordeiro, R. / Giuseppe, P.O. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
Sao Paulo Research Foundation (FAPESP)2016/00740-2 Brazil
CitationJournal: J. Mol. Biol. / Year: 2019
Title: N-glycan Utilization by Bifidobacterium Gut Symbionts Involves a Specialist beta-Mannosidase.
Authors: Cordeiro, R.L. / Pirolla, R.A.S. / Persinoti, G.F. / Gozzo, F.C. / de Giuseppe, P.O. / Murakami, M.T.
History
DepositionOct 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BlMan5B
B: BlMan5B


Theoretical massNumber of molelcules
Total (without water)99,2112
Polymers99,2112
Non-polymers00
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-16 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.395, 102.239, 171.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 26 or resid 28...
21(chain B and (resid 0 through 26 or resid 28...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 0 through 26 or resid 28...A0 - 26
121(chain A and (resid 0 through 26 or resid 28...A28 - 64
131(chain A and (resid 0 through 26 or resid 28...A66 - 108
141(chain A and (resid 0 through 26 or resid 28...A111 - 112
151(chain A and (resid 0 through 26 or resid 28...A154 - 228
161(chain A and (resid 0 through 26 or resid 28...A230 - 265
171(chain A and (resid 0 through 26 or resid 28...A267 - 2317
181(chain A and (resid 0 through 26 or resid 28...A319317
191(chain A and (resid 0 through 26 or resid 28...A319 - 416
211(chain B and (resid 0 through 26 or resid 28...B0 - 26
221(chain B and (resid 0 through 26 or resid 28...B28 - 64
231(chain B and (resid 0 through 26 or resid 28...B66 - 108
241(chain B and (resid 0 through 26 or resid 28...B111 - 112
251(chain B and (resid 0 through 26 or resid 28...B154 - 228
261(chain B and (resid 0 through 26 or resid 28...B230 - 265
271(chain B and (resid 0 through 26 or resid 28...B267 - 2317
281(chain B and (resid 0 through 26 or resid 28...B319317
291(chain B and (resid 0 through 26 or resid 28...B319 - 416

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Components

#1: Protein BlMan5B


Mass: 49605.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (strain DJO10A) (bacteria)
Strain: DJO10A / Gene: BLD_0195 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3DQP5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 3.33 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 273.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium citrate pH 4.5 and 12-16% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.8→43.894 Å / Num. obs: 122700 / % possible obs: 99.7 % / Redundancy: 5.143 % / Biso Wilson estimate: 28.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.092 / Χ2: 1.116 / Net I/σ(I): 12.47 / Num. measured all: 631088
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.915.0031.5921.059751719626194920.6911.77699.3
1.91-2.044.8880.8022.039042118538184970.8790.89899.8
2.04-2.25.3750.453.929253917241172180.9540.49899.9
2.2-2.415.2860.276.38406615919159030.9810.399.9
2.41-2.74.8560.1619.427030214490144780.9910.18199.9
2.7-3.115.5130.08817.427047612791127830.9970.09799.9
3.11-3.815.3430.04530.895821610904108960.9990.05199.9
3.81-5.374.8310.03142.5241156855285190.9990.03499.6
5.37-43.8945.3710.02750.1726395496949140.9990.0398.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.894 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.41
RfactorNum. reflection% reflection
Rfree0.203 6113 4.99 %
Rwork0.1836 --
obs0.1846 122585 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.57 Å2 / Biso mean: 44.2709 Å2 / Biso min: 23.25 Å2
Refinement stepCycle: final / Resolution: 1.8→43.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6530 0 0 595 7125
Biso mean---46.77 -
Num. residues----836
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3749X-RAY DIFFRACTION7.672TORSIONAL
12B3749X-RAY DIFFRACTION7.672TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8002-1.82070.49161730.45243734390798
1.8207-1.84210.44932170.4043860407799
1.8421-1.86460.3952240.372437914015100
1.8646-1.88820.34772080.355538244032100
1.8882-1.9130.31011790.340138364015100
1.913-1.93920.34952150.328738724087100
1.9392-1.96690.34172220.304738094031100
1.9669-1.99630.32582160.304338154031100
1.9963-2.02750.3292200.272238164036100
2.0275-2.06070.3161880.245838614049100
2.0607-2.09630.23652000.224338934093100
2.0963-2.13440.24772130.21438494062100
2.1344-2.17540.24321910.211138764067100
2.1754-2.21980.21461990.196538874086100
2.2198-2.26810.20011970.186238584055100
2.2681-2.32090.19592220.181338434065100
2.3209-2.37890.21072150.178438594074100
2.3789-2.44320.2072120.177738614073100
2.4432-2.51510.20651770.170939144091100
2.5151-2.59630.21182040.170938984102100
2.5963-2.6890.16621860.161339174103100
2.689-2.79670.18532110.166338654076100
2.7967-2.92390.21762120.182639054117100
2.9239-3.07810.21851880.184139154103100
3.0781-3.27090.21092010.182539354136100
3.2709-3.52330.18841960.178339454141100
3.5233-3.87770.17171810.156239644145100
3.8777-4.43830.14381960.130939894185100
4.4383-5.590.14992280.13339574185100
5.59-43.90730.15452220.15774124434698
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)
11.225-0.50250.23671.3947-0.45691.2463-0.0225-0.00430.0378-0.03910.20490.3463-0.3059-0.2931-0.18320.56770.02370.00590.28140.08740.2984-21.27648.434-27.511
20.9426-0.42580.27210.9199-0.22510.61440.0085-0.0068-0.05350.06180.0244-0.07720.11020.0857-0.04040.524-0.028-0.00480.2236-0.01720.201811.34615.925-19.425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 19:416 )A19 - 416
2X-RAY DIFFRACTION2( CHAIN B AND RESID 15:417 )B15 - 417

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