[English] 日本語
Yorodumi
- PDB-6d3q: Crystal structure of Escherichia coli enolase complexed with a na... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d3q
TitleCrystal structure of Escherichia coli enolase complexed with a natural inhibitor SF2312.
ComponentsEnolase
KeywordsLYASE/LYASE inhibitor / Enolase / complex / natural inhibitor / SF2312 / LYASE / LYASE-LYASE inhibitor complex
Function / homology
Function and homology information


bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / magnesium ion binding / cell surface ...bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / magnesium ion binding / cell surface / protein homodimerization activity / extracellular region / identical protein binding / membrane / cytosol
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / 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
Chem-4NG / Enolase / Enolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsErlandsen, H. / Krucinska, J. / Hazeen, A. / Wright, D.
CitationJournal: Sci Rep / Year: 2019
Title: Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate.
Authors: Krucinska, J. / Lombardo, M.N. / Erlandsen, H. / Hazeen, A. / Duay, S.S. / Pattis, J.G. / Robinson, V.L. / May, E.R. / Wright, D.L.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enolase
C: Enolase
B: Enolase
E: Enolase
F: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,82141
Polymers278,7346
Non-polymers3,08735
Water9,368520
1
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,77912
Polymers92,9112
Non-polymers86810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-90 kcal/mol
Surface area29160 Å2
MethodPISA
2
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,97514
Polymers92,9112
Non-polymers1,06412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-98 kcal/mol
Surface area29420 Å2
MethodPISA
3
E: Enolase
F: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,06715
Polymers92,9112
Non-polymers1,15613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-113 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.751, 142.071, 207.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 6 molecules ACBEFD

#1: Protein
Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 46455.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eno / Production host: Escherichia coli (E. coli)
References: UniProt: B7MLA0, UniProt: P0A6P9*PLUS, phosphopyruvate hydratase

-
Non-polymers , 5 types, 555 molecules

#2: Chemical
ChemComp-4NG / [(3S,5S)-1,5-dihydroxy-2-oxopyrrolidin-3-yl]phosphonic acid


Mass: 197.083 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.3 M Ammonium Sulfate, 0.2 M Na/K tartrate, 0.1M Mes pH 6.0 and 2 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2017
Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.24→207.28 Å / Num. obs: 147731 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.098 / Rrim(I) all: 0.25 / Net I/σ(I): 4.6
Reflection shellResolution: 2.24→2.34 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.444 / Num. unique obs: 17855 / CC1/2: 0.958 / Rpim(I) all: 0.142 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BFY

6bfy


Resolution: 2.24→207.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.348 / SU ML: 0.132 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.187
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 7420 5 %RANDOM
Rwork0.163 ---
obs0.1657 140311 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.57 Å2 / Biso mean: 38.102 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å20 Å2
2--1.35 Å20 Å2
3----3.38 Å2
Refinement stepCycle: final / Resolution: 2.24→207.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19500 0 174 520 20194
Biso mean--47.68 32.04 -
Num. residues----2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01919896
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218938
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.97426786
X-RAY DIFFRACTIONr_angle_other_deg1.0742.99844069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65652623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.65625.778810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.177153566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0471572
X-RAY DIFFRACTIONr_chiral_restr0.1110.23031
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023589
LS refinement shellResolution: 2.244→2.302 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 518 -
Rwork0.219 10318 -
all-10836 -
obs--99.66 %

+
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