[English] 日本語
Yorodumi
- PDB-8bou: Crystal structure of Blautia producta GH94 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bou
TitleCrystal structure of Blautia producta GH94
ComponentsN,N'-diacetylchitobiose phosphorylase
KeywordsHYDROLASE / Glycoside Hydrolase Family 94
Function / homology
Function and homology information


glycosyltransferase activity / methyltransferase activity / carbohydrate binding / methylation / carbohydrate metabolic process / nucleic acid binding
Similarity search - Function
N,N'-diacetylchitobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / : / Glycosyl hydrolase 94 / Glycosyl hydrolase 94, supersandwich domain / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / N-6 Adenine-specific DNA methylases signature. ...N,N'-diacetylchitobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / : / Glycosyl hydrolase 94 / Glycosyl hydrolase 94, supersandwich domain / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Six-hairpin glycosidase-like superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
ACETATE ION / N,N'-diacetylchitobiose phosphorylase
Similarity search - Component
Biological speciesBlautia producta ATCC 27340 = DSM 2950 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLevy, C.W.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR32876/PFN/20/1471/2020 India
CitationJournal: To Be Published
Title: Blautia producta is a competent degrader among human gut Firmicutes for utilizing dietary beta mixed linkage glucan
Authors: Singh, R.P. / Thankur, R. / Wagstaff, B. / Kumar, G. / Kurata, R. / Patel, D. / Miyazaki, T. / Levy, C.W. / Field, R.A.
History
DepositionNov 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N,N'-diacetylchitobiose phosphorylase
B: N,N'-diacetylchitobiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,75714
Polymers187,7172
Non-polymers1,04012
Water12,701705
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, PISA analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-64 kcal/mol
Surface area53330 Å2
Unit cell
Length a, b, c (Å)98.460, 135.290, 166.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein N,N'-diacetylchitobiose phosphorylase


Mass: 93858.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blautia producta ATCC 27340 = DSM 2950 (bacteria)
Gene: E5259_00910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G5MNS2

-
Non-polymers , 7 types, 717 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M carboxylic acids, 0.1 M Imidazole MES buffer pH 6.5, 60% precipitant mix 3 (40% v/v Glycerol, 20% w/v PEG 4000) [Morpheus G3, Molecular Dimensions]
Temp details: Cold room

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.32→52.56 Å / Num. obs: 97018 / % possible obs: 99.95 % / Redundancy: 11.7 % / Biso Wilson estimate: 55.83 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.046 / Net I/σ(I): 10.92
Reflection shellResolution: 2.32→2.403 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.699 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 9562 / CC1/2: 0.602 / CC star: 0.867 / Rpim(I) all: 0.4926 / % possible all: 99.92

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CQT

2cqt


Resolution: 2.32→52.56 Å / SU ML: 0.3329 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 4886 5.04 %
Rwork0.1776 92104 -
obs0.1798 96990 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.41 Å2
Refinement stepCycle: LAST / Resolution: 2.32→52.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12952 0 62 705 13719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002413429
X-RAY DIFFRACTIONf_angle_d0.547618196
X-RAY DIFFRACTIONf_chiral_restr0.04291844
X-RAY DIFFRACTIONf_plane_restr0.00412395
X-RAY DIFFRACTIONf_dihedral_angle_d5.10081819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.37411540.32153030X-RAY DIFFRACTION99.87
2.35-2.370.34821700.30683006X-RAY DIFFRACTION99.91
2.37-2.40.33081640.29883031X-RAY DIFFRACTION99.97
2.4-2.430.33041640.28213023X-RAY DIFFRACTION100
2.43-2.470.32421700.28823070X-RAY DIFFRACTION100
2.47-2.50.30941580.27293003X-RAY DIFFRACTION100
2.5-2.530.31361540.27453086X-RAY DIFFRACTION100
2.53-2.570.35891600.28423012X-RAY DIFFRACTION99.97
2.57-2.610.34231670.2773032X-RAY DIFFRACTION99.97
2.61-2.660.31411710.25333067X-RAY DIFFRACTION100
2.66-2.70.31041710.2433003X-RAY DIFFRACTION100
2.7-2.750.2821630.22493075X-RAY DIFFRACTION100
2.75-2.80.27081680.21293018X-RAY DIFFRACTION100
2.8-2.860.25711500.20543045X-RAY DIFFRACTION100
2.86-2.920.25891500.20753069X-RAY DIFFRACTION100
2.92-2.990.27721570.2023082X-RAY DIFFRACTION100
2.99-3.070.25721750.20663042X-RAY DIFFRACTION100
3.07-3.150.26851570.21223059X-RAY DIFFRACTION99.97
3.15-3.240.24621610.20363047X-RAY DIFFRACTION100
3.24-3.350.24621590.18673075X-RAY DIFFRACTION99.94
3.35-3.470.22631730.18013067X-RAY DIFFRACTION99.97
3.47-3.60.24521820.1713027X-RAY DIFFRACTION100
3.6-3.770.24281570.17533103X-RAY DIFFRACTION100
3.77-3.970.2061560.16083093X-RAY DIFFRACTION100
3.97-4.220.1991640.13823100X-RAY DIFFRACTION100
4.22-4.540.14981750.12453075X-RAY DIFFRACTION100
4.54-50.15151560.12413134X-RAY DIFFRACTION99.97
5-5.720.1861590.14253147X-RAY DIFFRACTION100
5.72-7.20.19931640.16453173X-RAY DIFFRACTION100
7.2-52.560.16921570.15953310X-RAY DIFFRACTION99.54
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)
10.952171640460.2301466108780.05598362994051.283728098150.189771645140.602947209138-0.08846417666710.03291602761650.0587955692549-0.03900211930720.0856700327032-0.0210354777855-0.1608686354760.06544750419366.42812950265E-50.632268956976-0.0159250152216-0.03509540126470.573976840334-0.003338659830810.55012719086196.873082127189.6881869617110.43392482
21.12055073144-0.0248892454799-0.1430402977521.43182844561-0.3212586267120.78548254588-0.06994628575430.08011768925640.2463816778480.02690011014080.110495482620.461830355568-0.266455868545-0.2477196601467.0068157119E-50.7201294736540.164574585572-0.03304573107320.716653418480.03033589018430.8706374225259.9381051851101.202815578113.730787656
30.448498905055-0.1492819565520.09738815538031.405677620730.09980192374930.975842839059-0.0375722525651-0.0820343193139-0.04369619234680.2229595241030.05150087762360.0755213118639-0.0452683061519-0.0623126657464-3.56376985361E-50.5629039378470.02294469862230.005219056483540.5744860998790.007287808328370.53290442437183.522959695958.2056251983123.48162895
40.769412081450.06360836503040.0279330969350.9945480427720.1943872328410.664541395915-0.06054686724530.151471156525-0.0686955966466-0.1757652781210.0403690725961-0.0105681427371-0.03512025116820.02659114742423.33059439288E-60.540609361789-0.02830972352440.0182155356110.605844655964-0.07353410412620.51987411999287.536850235346.427753950786.6201210356
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 340 )AA18 - 3401 - 323
22chain 'A' and (resid 341 through 824 )AA341 - 824324 - 807
33chain 'B' and (resid 20 through 340 )BF20 - 3401 - 321
44chain 'B' and (resid 341 through 824 )BF341 - 824322 - 805

+
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