[English] 日本語
Yorodumi
- PDB-4jn8: Crystal structure of an enolase (putative galactarate dehydratase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jn8
TitleCrystal structure of an enolase (putative galactarate dehydratase, target efi-500740) from agrobacterium radiobacter, bound sulfate, no metal ion, ordered active site
ComponentsENOLASE
KeywordsLYASE / ENOLASE / PUTATIVE GALACTARATE DEHYDRATASE / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


galactarate dehydratase activity / isomerase activity
Similarity search - Function
Galactarate dehydratase 3 / : / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain ...Galactarate dehydratase 3 / : / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAgrobacterium radiobacter K84 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVetting, M.W. / Groninger-Poe, F. / Bouvier, J.T. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Groninger-Poe, F. / Bouvier, J.T. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of an enolase (putative galactarate dehydratase, target efi-500740) from agrobacterium radiobacter, bound sulfate, no metal ion, ordered active site
Authors: Vetting, M.W. / Groninger-Poe, F. / Bouvier, J.T. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, ...Authors: Vetting, M.W. / Groninger-Poe, F. / Bouvier, J.T. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,35411
Polymers44,6851
Non-polymers66910
Water10,178565
1
A: ENOLASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)362,83388
Polymers357,4778
Non-polymers5,35580
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area59830 Å2
ΔGint-474 kcal/mol
Surface area80770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.044, 124.044, 114.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-743-

HOH

21A-1059-

HOH

Detailsbiological unit is an octamer

-
Components

#1: Protein ENOLASE


Mass: 44684.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium radiobacter K84 (bacteria)
Strain: K84 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9JNP7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (20 mM Tris pH 7.9, 5 mM MgCl2, 0.1 M NaCl); Reservoir (2.0 M Ammonium Sulfate, 0.1 M Bis-Tris pH 5.5); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM MgCl), temperature ...Details: Protein (20 mM Tris pH 7.9, 5 mM MgCl2, 0.1 M NaCl); Reservoir (2.0 M Ammonium Sulfate, 0.1 M Bis-Tris pH 5.5); Cryoprotection (Reservoir, + 20% ethylene glycol and 50 mM MgCl), temperature 298K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 7, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→87.712 Å / Num. all: 87340 / Num. obs: 87340 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.4814.40.7241181562126280.724100
1.48-1.5714.50.511.5173166119560.51100
1.57-1.6714.60.372163801112400.37100
1.67-1.8114.70.2543154047105060.254100
1.81-1.9814.80.1873.914348596740.187100
1.98-2.2114.90.1564.113089287680.156100
2.21-2.56150.1394.711675278080.139100
2.56-3.1314.90.0979862366070.09100
3.13-4.4314.80.04413.87687651950.044100
4.43-21.18914.10.03814.54177029580.03899.1

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RR1

3rr1


Resolution: 1.4→21.189 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.9333 / SU ML: 0.07 / σ(F): 0 / σ(I): 0 / Phase error: 12.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1457 4380 5.02 %RANDOM
Rwork0.1285 ---
all0.1294 87337 --
obs0.1294 87337 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.71 Å2 / Biso mean: 10.6538 Å2 / Biso min: 0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.4→21.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 37 565 3756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083323
X-RAY DIFFRACTIONf_angle_d1.3024520
X-RAY DIFFRACTIONf_chiral_restr0.077466
X-RAY DIFFRACTIONf_plane_restr0.008600
X-RAY DIFFRACTIONf_dihedral_angle_d12.6171233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.41590.19411520.181327392891
1.4159-1.43260.20641570.180327052862
1.4326-1.450.21961580.171227102868
1.45-1.46840.16991220.162227402862
1.4684-1.48770.17821610.155527262887
1.4877-1.50810.18061330.143427652898
1.5081-1.52960.14111390.14527212860
1.5296-1.55240.15541300.137827702900
1.5524-1.57670.16441350.133927322867
1.5767-1.60250.15551380.132227412879
1.6025-1.63020.15281410.128527602901
1.6302-1.65980.15831430.129627572900
1.6598-1.69170.13731420.125227542896
1.6917-1.72620.15511370.125727582895
1.7262-1.76370.14441340.116127482882
1.7637-1.80470.12941620.112227272889
1.8047-1.84980.11691490.111827462895
1.8498-1.89980.13951490.114927592908
1.8998-1.95570.13091470.115227302877
1.9557-2.01880.12341330.113227852918
2.0188-2.09090.15521340.107527732907
2.0909-2.17450.12131680.105727692937
2.1745-2.27340.11831440.106227742918
2.2734-2.39310.13181580.108527572915
2.3931-2.54280.13041400.112427862926
2.5428-2.73870.12831570.114227782935
2.7387-3.01360.14121330.121628282961
3.0136-3.44810.12981530.12828192972
3.4481-4.33810.12751700.119828323002
4.3381-21.19190.20361610.186729683129

+
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://pdbjlvh1.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