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- PDB-7ugh: Crystal Structure of enolase family protein from Naegleria fowler... -

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Basic information

Entry
Database: PDB / ID: 7ugh
TitleCrystal Structure of enolase family protein from Naegleria fowleri with bound 2-phosphoglyceric acid
ComponentsPhosphopyruvate hydratase
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphopyruvate hydratase


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

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Non-polymers , 5 types, 656 molecules

#2: Chemical ChemComp-2PG / 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


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


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


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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