[English] 日本語
Yorodumi
- PDB-6mp2: Crystal structure of BlMan5B solved by SIRAS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mp2
TitleCrystal structure of BlMan5B solved by SIRAS
ComponentsBlMan5B
KeywordsHYDROLASE / Family GH5 / subfamily 18 / beta-mannosidase
Function / homologyGlycoside hydrolase superfamily / Glycosyl hydrolase
Function and homology information
Biological speciesBifidobacterium longum DJO10A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SIRAS / Resolution: 1.98 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: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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)100,06410
Polymers99,3272
Non-polymers7378
Water9,872548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-11 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.570, 101.918, 171.585
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 42 or resid 44...
21(chain B and (resid 19 through 42 or resid 44...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 19 through 42 or resid 44...A19 - 42
121(chain A and (resid 19 through 42 or resid 44...A44 - 46
131(chain A and (resid 19 through 42 or resid 44...A48 - 147
141(chain A and (resid 19 through 42 or resid 44...A149 - 196
151(chain A and (resid 19 through 42 or resid 44...A198 - 248
161(chain A and (resid 19 through 42 or resid 44...A250 - 296
171(chain A and (resid 19 through 42 or resid 44...A298 - 356
181(chain A and (resid 19 through 42 or resid 44...A358 - 437
211(chain B and (resid 19 through 42 or resid 44...B19 - 42
221(chain B and (resid 19 through 42 or resid 44...B44 - 46
231(chain B and (resid 19 through 42 or resid 44...B48 - 147
241(chain B and (resid 19 through 42 or resid 44...B149 - 196
251(chain B and (resid 19 through 42 or resid 44...B298 - 356
261(chain B and (resid 19 through 42 or resid 44...B358 - 437

-
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 DJO10A (bacteria)
Strain: DJO10A / Gene: BLD_0195 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3DQP5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
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: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.98→48.85 Å / Num. obs: 92510 / % possible obs: 98.2 % / Redundancy: 4.974 % / Biso Wilson estimate: 31.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.085 / Χ2: 1.028 / Net I/σ(I): 13.51 / Num. measured all: 460151
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
1.98-2.13.1881.0491.314454815007139730.661.24893.1
2.1-2.244.0710.4992.925621514185138100.8910.57397.4
2.24-2.424.6870.3434.66113413198130420.9510.38798.8
2.42-2.655.6410.2447.136846412162121370.9810.26999.8
2.65-2.975.8490.13912.016474811078110690.9930.15399.9
2.97-3.425.9090.07320.757769978297760.9970.0899.9
3.42-4.195.8030.04233.2548525836783620.9990.04799.9
4.19-5.95.7160.03639.937490656765590.9990.03999.9
5.9-48.855.6210.03144.9621258381537820.9990.03499.1

-
Phasing

PhasingMethod: SIRAS

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
SHELXphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→48.85 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1886 4528 4.9 %
Rwork0.1658 87918 -
obs0.167 92446 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.92 Å2 / Biso mean: 42.6559 Å2 / Biso min: 21.01 Å2
Refinement stepCycle: final / Resolution: 1.98→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 48 548 7148
Biso mean--55.5 47.31 -
Num. residues----838
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3814X-RAY DIFFRACTION8.448TORSIONAL
12B3814X-RAY DIFFRACTION8.448TORSIONAL
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 (%)
1.9797-2.00220.39991380.36892624276289
2.0022-2.02580.35781550.352707286293
2.0258-2.05050.33661500.31722729287993
2.0505-2.07650.35761540.29132797295195
2.0765-2.10380.28421440.26152805294997
2.1038-2.13260.2831490.25232880302996
2.1326-2.16310.29251330.24032883301698
2.1631-2.19540.27631460.22192886303297
2.1954-2.22970.24851530.20642851300497
2.2297-2.26620.20111530.2122913306698
2.2662-2.30530.2311520.19192915306799
2.3053-2.34720.20241460.182930307699
2.3472-2.39240.24571270.18622970309799
2.3924-2.44120.2071240.1792943306799
2.4412-2.49430.21691520.174629693121100
2.4943-2.55230.21161410.171329773118100
2.5523-2.61610.21421370.175729573094100
2.6161-2.68680.20921450.166129783123100
2.6868-2.76590.17411620.162429853147100
2.7659-2.85520.17871530.167429703123100
2.8552-2.95720.20521570.171229823139100
2.9572-3.07560.19631470.172229833130100
3.0756-3.21550.18971670.171429663133100
3.2155-3.3850.17871440.161630223166100
3.385-3.5970.18381570.151729813138100
3.597-3.87470.17761650.141730043169100
3.8747-4.26440.13951790.12130373216100
4.2644-4.8810.12261650.112330163181100
4.881-6.14760.15221660.138530673233100
6.1476-48.8650.16321670.1483191335899
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)
11.46940.3748-0.03110.92290.21071.6274-0.0026-0.08920.11080.03230.0972-0.1849-0.35330.3607-0.09660.4341-0.0144-0.00430.3053-0.05420.238860.05947.69114.221
21.0670.52080.53120.87050.45571.52770.0262-0.0652-0.04030.0124-0.02780.07590.152-0.2289-0.00010.33770.04350.00630.23970.02070.183226.79316.174105.593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 19:417 )A19 - 417
2X-RAY DIFFRACTION2( CHAIN B AND RESID 19:417 )B19 - 417

+
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