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- PDB-6mp7: Crystal structure of the E257A mutant of BlMan5B in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6mp7
TitleCrystal structure of the E257A mutant of BlMan5B in complex with GlcNAc (soaking)
ComponentsBlMan5B
KeywordsHYDROLASE / Family GH5 / subfamily 18 / beta-mannosidase
Function / homologyGlycoside hydrolase superfamily / CITRATE ANION / Glycosyl hydrolase
Function and homology information
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8666
Polymers99,2112
Non-polymers6554
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-16 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.805, 101.247, 172.935
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 19 through 84 or resid 86...
21(chain B and (resid 19 through 84 or resid 86...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 19 through 84 or resid 86...A19 - 84
121(chain A and (resid 19 through 84 or resid 86...A86 - 127
131(chain A and (resid 19 through 84 or resid 86...A130 - 148
141(chain A and (resid 19 through 84 or resid 86...A293 - 409
151(chain A and (resid 19 through 84 or resid 86...A293 - 409
161(chain A and (resid 19 through 84 or resid 86...A411 - 428
171(chain A and (resid 19 through 84 or resid 86...A430 - 439
211(chain B and (resid 19 through 84 or resid 86...B19 - 84
221(chain B and (resid 19 through 84 or resid 86...B86 - 127
231(chain B and (resid 19 through 84 or resid 86...B130 - 148
241(chain B and (resid 19 through 84 or resid 86...B19 - 439
251(chain B and (resid 19 through 84 or resid 86...B293 - 409
261(chain B and (resid 19 through 84 or resid 86...B411 - 428
271(chain B and (resid 19 through 84 or resid 86...B430 - 439

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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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
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: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.75→48.585 Å / Num. obs: 123099 / % possible obs: 99.2 % / Redundancy: 6.038 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Χ2: 1.103 / Net I/σ(I): 13.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.865.1611.5661.01192760.6061.74197.3
1.86-1.985.370.7812.03186080.8840.86599.4
1.98-2.146.3550.4314.2173330.9370.46999.9
2.14-2.356.4720.2616.95160170.9750.28499.8
2.35-2.625.9730.16610.22145580.9870.18299.8
2.62-3.036.8370.09318.43128740.9960.10199.6
3.03-3.76.5550.05431109430.9980.05999.6
3.7-5.225.9020.03344.7685840.9990.03699.6
5.22-48.5856.6720.02952.5549060.9990.03298.1

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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
Starting model: 6MP2

6mp2


Resolution: 1.75→48.585 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.16
RfactorNum. reflection% reflection
Rfree0.1941 6028 4.9 %
Rwork0.1724 --
obs0.1734 123040 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.99 Å2 / Biso mean: 34.306 Å2 / Biso min: 16.78 Å2
Refinement stepCycle: final / Resolution: 1.75→48.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 44 589 7238
Biso mean--36.75 41.77 -
Num. residues----847
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3789X-RAY DIFFRACTION6.863TORSIONAL
12B3789X-RAY DIFFRACTION6.863TORSIONAL
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 (%)
1.75-1.76990.36331900.31733686387696
1.7699-1.79080.36121930.29553766395996
1.7908-1.81260.28482100.29153791400198
1.8126-1.83550.36582180.2943816403497
1.8355-1.85970.30311760.27953809398599
1.8597-1.88520.29321930.2593869406299
1.8852-1.91210.27011890.25263865405499
1.9121-1.94060.29392040.23793885408999
1.9406-1.9710.2441880.21738334021100
1.971-2.00330.23462350.211339114146100
2.0033-2.03780.26371960.198738674063100
2.0378-2.07490.23541930.197239044097100
2.0749-2.11480.24391890.190839264115100
2.1148-2.1580.21442040.190539244128100
2.158-2.20490.21471690.181538834052100
2.2049-2.25620.20011970.178139464143100
2.2562-2.31260.20661880.175638914079100
2.3126-2.37510.18542220.167638914113100
2.3751-2.4450.211950.170539244119100
2.445-2.52390.20722220.17538964118100
2.5239-2.61410.20831780.169739724150100
2.6141-2.71880.21451930.161938894082100
2.7188-2.84250.18112280.175839074135100
2.8425-2.99230.20791920.177339664158100
2.9923-3.17980.18832170.175539304147100
3.1798-3.42520.18292150.16133927414299
3.4252-3.76980.18692040.152839724176100
3.7698-4.3150.13251990.132140024201100
4.315-5.43530.15132230.131740284251100
5.4353-48.60330.16072080.16334136434498
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)
11.4122-0.06940.00391.3822-0.43511.2810.03890.09220.1041-0.1763-0.0857-0.257-0.04060.23640.05030.18720.00550.02420.199-0.00320.187612.622-16.11320.954
21.16180.22080.17850.74440.03891.04940.0257-0.0756-0.1022-0.03980.02690.12410.1666-0.1382-0.05410.2223-0.0034-0.01630.1920.03680.2-19.53-48.47326.29
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:424 )A-1 - 424
2X-RAY DIFFRACTION2( CHAIN B AND RESID -1:419 )B-1 - 419

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