[English] 日本語
Yorodumi
- PDB-8u01: Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u01
TitleCrystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domain Containing Protein from Phocaeicola plebeius
ComponentsGlycosyl hydrolase family 2, sugar binding domain protein
KeywordsHYDROLASE / beta galactosidase / TIM barrel Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / D-tagatose / Glycosyl hydrolase family 2, sugar binding domain protein
Similarity search - Component
Biological speciesPhocaeicola plebeius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsKim, Y. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domain Containing Protein from Phocaeicola plebeius
Authors: Kim, Y. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl hydrolase family 2, sugar binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,25741
Polymers104,0011
Non-polymers3,25640
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-25 kcal/mol
Surface area33950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.110, 230.110, 230.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11A-1019-

PEG

21A-1231-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glycosyl hydrolase family 2, sugar binding domain protein


Mass: 104001.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola plebeius (bacteria) / Gene: BACPLE_01374 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: B5CXD3
#9: Sugar ChemComp-TAG / D-tagatose / Tagatose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 8 types, 228 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.93 Å3/Da / Density % sol: 75.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, 30% v/v PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→72.8 Å / Num. obs: 42107 / % possible obs: 100 % / Redundancy: 26 % / Biso Wilson estimate: 44.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.027 / Rrim(I) all: 0.139 / Net I/σ(I): 28.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 2039 / CC1/2: 0.974 / Rpim(I) all: 0.105 / Rrim(I) all: 0.534 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 3→69.38 Å / SU ML: 0.2713 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.1531
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1861 2129 5.06 %
Rwork0.1534 39908 -
obs0.1551 42037 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.3 Å2
Refinement stepCycle: LAST / Resolution: 3→69.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7177 0 207 189 7573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317588
X-RAY DIFFRACTIONf_angle_d0.564510222
X-RAY DIFFRACTIONf_chiral_restr0.04271071
X-RAY DIFFRACTIONf_plane_restr0.00451310
X-RAY DIFFRACTIONf_dihedral_angle_d13.94082774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.30491430.23582591X-RAY DIFFRACTION99.27
3.07-3.150.24931480.20882599X-RAY DIFFRACTION99.96
3.15-3.230.29761460.19542612X-RAY DIFFRACTION99.96
3.23-3.330.22151280.19472627X-RAY DIFFRACTION100
3.33-3.440.24891300.18492637X-RAY DIFFRACTION100
3.44-3.560.19861340.17852609X-RAY DIFFRACTION99.89
3.56-3.70.2221590.16652621X-RAY DIFFRACTION99.93
3.7-3.870.18971380.14242623X-RAY DIFFRACTION99.93
3.87-4.070.16341340.13242643X-RAY DIFFRACTION100
4.07-4.330.1671440.11872670X-RAY DIFFRACTION100
4.33-4.660.14961490.10782641X-RAY DIFFRACTION100
4.66-5.130.11871460.11122670X-RAY DIFFRACTION99.96
5.13-5.880.14741160.1322735X-RAY DIFFRACTION100
5.88-7.40.17491460.16282743X-RAY DIFFRACTION100
7.4-69.380.16371680.16992887X-RAY DIFFRACTION99.41
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)
10.4596153481110.1017871577590.2599277210910.739079239967-0.05448887156480.726000414968-0.0235204340021-0.004218448440580.0924978424743-0.0749158598298-0.00650241050105-0.0809162369206-0.138245656729-0.0337362850740.03561852414070.2850650800320.05850736681110.03104036044190.261517718947-0.03903410077960.326268552111123.35183834127.753167452141.1186240384
28.685095610777.072727322350.4528207913396.341827286550.01639265352630.6028271888740.176666810177-0.299884127252-0.09116402082860.321465901693-0.201189080092-0.2524323409670.0592838365304-0.06108092140070.0231730077160.3052496146360.112943088155-0.00855765622630.268599215221-0.03041275215580.311408033225135.87992197916.68219466768.4472753029
30.8921022221270.07944718408170.3333223862470.6386419045110.1418266068490.7413513691210.0157527711301-0.01915008768990.01534183850580.0047072862172-0.0251173741737-0.0593378149007-0.0106786588458-0.02845298887140.00989437956380.2482694382770.04768712383710.0022543159840.211039019927-0.03613956888380.225534500389117.1857352314.1114876559742.9131023134
43.773930218642.142520055791.512870486563.116775663441.148602120573.383025716120.182241694517-0.444601088335-0.2618528599510.102606181773-0.1163798916740.04201555281270.223358378397-0.435130152776-0.04051281378090.2851752308240.02514258871690.04142933350930.2590300318070.002791242292880.21920952960899.8318545405-19.353605810751.8029202276
52.831390167560.5771531810892.842426504331.158691272410.6705960995734.069546422290.1270026853290.110584663242-0.159535675506-0.09288011166340.07055157277790.2879794737220.233067942755-0.386207935526-0.3169717478210.2361589982970.009718516175090.0008042352935920.203505453776-0.0453465476210.36500785753687.1354275336-17.476280464820.2580236347
61.23445427341.76657260070.2951283457842.665976189630.8534721926741.77033408403-0.08525151811540.01193807658790.129179102535-0.1462972042180.03149533959290.227986464797-0.104119649512-0.247986111010.07381024857040.2009608239150.0302982253752-0.01361731080020.24464283848-0.06417873992760.26527869376994.0761554891-5.3557359268726.5242448043
72.636889583381.155139086370.8834251451973.86104035410.156338995592.64772465634-0.089964038708-0.06189171044710.312164113314-0.326804146774-0.0820732110260.40174829337-0.0721523797929-0.5707896806670.1507821018610.2842491287550.00257045347563-0.02355803500440.342082466186-0.09278115316240.30248874114683.3157484464-15.211950619119.240188616
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 213 )-2 - 2131 - 217
22chain 'A' and (resid 214 through 274 )214 - 274218 - 278
33chain 'A' and (resid 275 through 603 )275 - 603279 - 607
44chain 'A' and (resid 604 through 704 )604 - 704608 - 708
55chain 'A' and (resid 705 through 765 )705 - 765709 - 766
66chain 'A' and (resid 766 through 844 )766 - 844767 - 845
77chain 'A' and (resid 845 through 908 )845 - 908846 - 909

+
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