[English] 日本語
Yorodumi
- PDB-6mp7: Crystal structure of the E257A mutant of BlMan5B in complex with ... -

+
Open data


ID or keywords:

Loading...

-
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 / homologyGlycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more