[English] 日本語
Yorodumi
- PDB-7ugh: Crystal Structure of enolase family protein from Naegleria fowler... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ugh
TitleCrystal Structure of enolase family protein from Naegleria fowleri with bound 2-phosphoglyceric acid
ComponentsPhosphopyruvate hydrataseEnolase
KeywordsLYASE / SSGCID / enolase / 2-phosphoglyceric acid / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / magnesium ion binding
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, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
2-PHOSPHOGLYCERIC ACID / ACETATE ION / Phosphopyruvate hydratase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
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 enolase family protein from Naegleria fowleri with bound 2-phosphoglyceric acid
Authors: Bolejack, M.J. / DeBouver, N.D. / Morris, J.C. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphopyruvate hydratase
B: Phosphopyruvate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,78718
Polymers104,7142
Non-polymers1,07316
Water11,530640
1
A: Phosphopyruvate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8939
Polymers52,3571
Non-polymers5368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphopyruvate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8939
Polymers52,3571
Non-polymers5368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.860, 96.860, 216.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Phosphopyruvate hydratase / Enolase


Mass: 52356.973 Da / Num. of mol.: 2 / Fragment: NafoA.00379.a.B5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Strain: ATCC 30863 / Gene: NF0118810 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6A5BXC3, phosphopyruvate hydratase

-
Non-polymers , 5 types, 656 molecules

#2: Chemical ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID / 2-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein at 36 mg/mL was combined with 5 mM 2-PG and mixed 1:1 (0.2 uL protein and 0.2 uL precipitant) with 85 mM Tris/HCl pH 8.5, 25.5% (w/v) PEG4000, 15% glycerol, and 170 mM sodium acetate ...Details: Protein at 36 mg/mL was combined with 5 mM 2-PG and mixed 1:1 (0.2 uL protein and 0.2 uL precipitant) with 85 mM Tris/HCl pH 8.5, 25.5% (w/v) PEG4000, 15% glycerol, and 170 mM sodium acetate (JCSG TOP96 A11). Cryo: Direct. Puck: vfn4-7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→47.26 Å / Num. obs: 75148 / % possible obs: 98.9 % / Redundancy: 6.926 % / Biso Wilson estimate: 32.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.062 / Χ2: 0.938 / Net I/σ(I): 19.58 / Num. measured all: 520503
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
1.95-27.0770.5993.1638442551754320.8680.64698.5
2-2.067.0720.4554.237512538553040.9240.49198.5
2.06-2.127.0670.3445.4536557524351730.9530.3798.7
2.12-2.187.0570.2617.1235332507050070.970.28298.8
2.18-2.257.0360.2059.1834703499149320.9810.22198.8
2.25-2.337.0220.16411.0833173477647240.9890.17798.9
2.33-2.427.0350.13813.1632383464746030.9910.14899.1
2.42-2.527.0070.11614.9630882444944070.9940.12599.1
2.52-2.636.9710.09717.9129683429142580.9950.10599.2
2.63-2.766.9590.08121.3228468412440910.9970.08799.2
2.76-2.916.9140.06725.2126703388538620.9970.07299.4
2.91-3.086.8680.05629.4125425372737020.9980.06199.3
3.08-3.36.8490.0532.4324041353435100.9980.05499.3
3.3-3.566.7750.04436.7321978326332440.9980.04899.4
3.56-3.96.6920.0440.2620204303730190.9980.04399.4
3.9-4.366.7170.03742.1518370275427350.9990.0499.3
4.36-5.036.6710.03543.1316277246024400.9990.03899.2
5.03-6.176.6930.03442.3713962211220860.9990.03698.8
6.17-8.726.5280.03142.8110797168416540.9990.03498.2
8.72-47.265.8150.02941.81561110179650.9980.03294.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX4487refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4a3r

4a3r


Resolution: 1.95→47.26 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 1956 2.6 %
Rwork0.1527 73185 -
obs0.1537 75141 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.94 Å2 / Biso mean: 37.5154 Å2 / Biso min: 19.64 Å2
Refinement stepCycle: final / Resolution: 1.95→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 66 641 7366
Biso mean--47.36 42.69 -
Num. residues----870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.26341440.20435060520498
2-2.050.20771410.19035112525399
2.05-2.110.21351230.17785173529699
2.11-2.180.20981310.16145146527799
2.18-2.260.17451450.15325150529599
2.26-2.350.19691410.15735166530799
2.35-2.460.21211450.16255150529599
2.46-2.590.21091340.16725224535899
2.59-2.750.22821330.16815207534099
2.75-2.960.19371540.158552485402100
2.96-3.260.19211420.15915278542099
3.26-3.730.18111330.143253185451100
3.73-4.70.15341240.12275383550799
4.7-47.260.19491660.15655570573699
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)
12.38960.93460.60722.11820.78672.52510.0354-0.0352-0.49630.3295-0.00010.0070.35830.0881-0.07240.3407-0.0356-0.0050.22080.03620.3441-46.6161-8.4984-9.0972
21.62810.70710.12681.43880.34651.00050.0425-0.0123-0.23540.1526-0.02550.22620.225-0.1966-0.01420.2416-0.04850.02550.22740.00930.2932-56.6528-3.0175-14.3924
31.86650.7452-0.24262.1274-0.48082.25240.1591-0.2827-0.02720.4236-0.0972-0.27010.00490.2308-0.05490.2865-0.0126-0.06250.275-0.03580.2145-25.071513.1945-1.1128
40.922-0.148-0.1911.47160.22770.88110.0220.1105-0.1555-0.07340.0708-0.29720.14360.2602-0.07990.21660.0471-0.0210.3213-0.07180.2455-18.55220.1905-22.5125
52.1375-0.2192-0.25021.678-0.06563.37670.07450.0740.26850.0478-0.06110.2551-0.2664-0.1419-0.00530.17540.00950.00140.1437-0.00460.2388-48.711120.1411-19.8096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 233 through 286 )B233 - 286
2X-RAY DIFFRACTION2chain 'B' and (resid 287 through 512 )B287 - 512
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 232 )A77 - 232
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 555 )A233 - 555
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 232 )B79 - 232

+
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