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- PDB-6mpa: Crystal structure of BlMan5B in complex with GlcNAc (soaking) -

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Basic information

Entry
Database: PDB / ID: 6mpa
TitleCrystal structure 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: 1.9 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 1.4Mar 13, 2024Group: 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)99,7384
Polymers99,3272
Non-polymers4102
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-10 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.893, 101.378, 173.003
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 -1 through 22 or resid 24...
21(chain B and (resid -1 through 22 or resid 24...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTRPTRP(chain A and (resid -1 through 22 or resid 24...AA-1 - 2219 - 42
12VALVALVALVAL(chain A and (resid -1 through 22 or resid 24...AA24 - 6444 - 84
13METMETSERSER(chain A and (resid -1 through 22 or resid 24...AA67 - 12787 - 147
14LYSLYSPROPRO(chain A and (resid -1 through 22 or resid 24...AA130 - 271150 - 291
15PHEPHEARGARG(chain A and (resid -1 through 22 or resid 24...AA273 - 336293 - 356
16THRTHRALAALA(chain A and (resid -1 through 22 or resid 24...AA338 - 346358 - 366
17VALVALLEULEU(chain A and (resid -1 through 22 or resid 24...AA348 - 358368 - 378
18ARGARGGLUGLU(chain A and (resid -1 through 22 or resid 24...AA360 - 406380 - 426
19VALVALASPASP(chain A and (resid -1 through 22 or resid 24...AA408 - 421428 - 441
21SERSERTRPTRP(chain B and (resid -1 through 22 or resid 24...BB-1 - 2219 - 42
22VALVALVALVAL(chain B and (resid -1 through 22 or resid 24...BB24 - 6444 - 84
23METMETSERSER(chain B and (resid -1 through 22 or resid 24...BB67 - 12787 - 147
24LYSLYSPROPRO(chain B and (resid -1 through 22 or resid 24...BB130 - 271150 - 291
25PHEPHEARGARG(chain B and (resid -1 through 22 or resid 24...BB273 - 336293 - 356
26THRTHRALAALA(chain B and (resid -1 through 22 or resid 24...BB338 - 346358 - 366
27VALVALLEULEU(chain B and (resid -1 through 22 or resid 24...BB348 - 358368 - 378
28ARGARGGLUGLU(chain B and (resid -1 through 22 or resid 24...BB360 - 406380 - 426
29VALVALASPASP(chain B and (resid -1 through 22 or resid 24...BB408 - 421428 - 441

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Components

#1: Protein BlMan5B


Mass: 49663.609 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: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: 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.: 1
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.9→43.733 Å / Num. obs: 97455 / % possible obs: 99.9 % / Redundancy: 6.394 % / Biso Wilson estimate: 29.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.135 / Χ2: 1.083 / Net I/σ(I): 11.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.016.1321.6071.08155290.5371.75799.7
2.01-2.156.3840.8562.07146560.750.932100
2.15-2.336.1460.543.19136960.8750.59100
2.33-2.556.7510.355.23125970.9480.379100
2.55-2.856.610.2098.48114380.9830.227100
2.85-3.296.1780.10915.14101610.9950.119100
3.29-4.026.8460.05729.7486490.9980.061100
4.02-5.676.1920.04336.4567930.9990.047100
5.67-43.7336.4820.03543.9239360.9990.03899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.733 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.94
RfactorNum. reflection% reflection
Rfree0.2021 4830 4.96 %
Rwork0.1777 --
obs0.1789 97434 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.69 Å2 / Biso mean: 34.2081 Å2 / Biso min: 17.11 Å2
Refinement stepCycle: final / Resolution: 1.9→43.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6669 0 28 615 7312
Biso mean--49.39 41.6 -
Num. residues----854
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3789X-RAY DIFFRACTION7.912TORSIONAL
12B3789X-RAY DIFFRACTION7.912TORSIONAL
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 (%)
1.8999-1.92150.38311420.3263058320099
1.9215-1.94410.33871390.326730693208100
1.9441-1.96780.36691320.314530543186100
1.9678-1.99270.29511570.28230653222100
1.9927-2.01890.29061720.262530183190100
2.0189-2.04660.29641770.245330413218100
2.0466-2.07580.27031630.241430523215100
2.0758-2.10680.22231690.228430483217100
2.1068-2.13970.27631350.230130503185100
2.1397-2.17480.23581530.22630823235100
2.1748-2.21230.24891530.222330843237100
2.2123-2.25250.26371390.215630843223100
2.2525-2.29590.23141680.196830323200100
2.2959-2.34270.24221620.184230743236100
2.3427-2.39370.22431620.177730643226100
2.3937-2.44930.20751610.17830663227100
2.4493-2.51060.20871600.181631013261100
2.5106-2.57850.21751660.182730523218100
2.5785-2.65430.20691910.174630483239100
2.6543-2.740.21121710.170930873258100
2.74-2.83790.22281470.184530863233100
2.8379-2.95150.22671770.182930743251100
2.9515-3.08580.21671700.182631013271100
3.0858-3.24840.19971660.173930883254100
3.2484-3.45190.18421980.172330693267100
3.4519-3.71830.17661720.153831303302100
3.7183-4.09220.15381750.135331203295100
4.0922-4.68380.13181620.120531593321100
4.6838-5.89880.15081430.14932093352100
5.8988-43.7450.19591480.17143339348799
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)
11.3768-0.3202-0.21520.70680.13360.9950.01570.04290.09220.03610.01930.1134-0.1286-0.1201-0.03620.2128-0.00250.01720.16820.02970.1946-19.78248.568-25.896
21.47170.04950.1511.5176-0.25561.33480.0492-0.1231-0.1060.2623-0.0538-0.27970.04430.19410.01120.2265-0.0105-0.03450.186-0.00630.207112.48715.777-20.471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 19:421 )A19 - 421
2X-RAY DIFFRACTION2( CHAIN B AND RESID 19:429 )B19 - 429

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