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- PDB-8uel: Crystal structure of enolase from Litopenaeus vannamei -

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Basic information

Entry
Database: PDB / ID: 8uel
TitleCrystal structure of enolase from Litopenaeus vannamei
ComponentsEnolase
KeywordsLYASE / Litopenaeus vannamei / metal protein
Function / homologyPHOSPHOENOLPYRUVATE
Function and homology information
Biological speciesPenaeus vannamei (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChang, X. / Zhao, G.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2021YDF2100105 China
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Characterization and Structural Analyses of Enolase from Shrimp ( Litopenaeus vannamei ).
Authors: Chang, X. / Zhang, T. / Zang, J. / Lv, C. / Zhao, G.
History
DepositionOct 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,12110
Polymers94,4952
Non-polymers6258
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-79 kcal/mol
Surface area29110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.613, 86.571, 155.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Enolase


Mass: 47247.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Penaeus vannamei (Pacific white shrimp)
#2: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: (NH4)2SO4, MES pH 6.5, PEG 5000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.276911 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.276911 Å / Relative weight: 1
ReflectionResolution: 2.49→30 Å / Num. obs: 38505 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.077 / Rrim(I) all: 0.196 / Χ2: 1.104 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.90.64118710.8680.9640.2850.7020.58499.9
2.54-2.596.10.63118940.8770.9670.2740.6880.57799.8
2.59-2.646.30.6119000.8950.9720.2610.6650.58100
2.64-2.696.40.53919010.9050.9750.230.5870.603100
2.69-2.756.20.50318990.8980.9730.220.550.627100
2.75-2.826.60.43118870.9320.9820.180.4670.665100
2.82-2.896.40.37519320.9450.9860.160.4080.73100
2.89-2.966.50.34318920.9480.9870.1460.3740.757100
2.96-3.056.70.30518860.9580.9890.1270.3310.816100
3.05-3.156.60.25819140.9660.9910.1090.2810.908100
3.15-3.266.50.23119060.9710.9930.0990.2510.984100
3.26-3.396.30.20119170.9760.9940.0870.2191.111100
3.39-3.556.60.18119040.9770.9940.0770.1971.29199.8
3.55-3.736.40.15819380.9840.9960.0680.1731.39799.9
3.73-3.976.60.14419170.9840.9960.0610.1571.728100
3.97-4.276.40.1319440.9860.9970.0560.1411.826100
4.27-4.76.40.11619600.9880.9970.050.1261.923100
4.7-5.386.40.11119510.9840.9960.0480.1211.695100
5.38-6.766.30.10219870.9880.9970.0440.1111.393100
6.76-105.80.08621050.9920.9980.0390.0941.714100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data scaling
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→29.68 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2244 2000 5.2 %
Rwork0.1683 --
obs0.1712 38440 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6618 0 34 369 7021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086754
X-RAY DIFFRACTIONf_angle_d0.9259112
X-RAY DIFFRACTIONf_dihedral_angle_d6.36920
X-RAY DIFFRACTIONf_chiral_restr0.0511020
X-RAY DIFFRACTIONf_plane_restr0.0081188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.29741460.21882531X-RAY DIFFRACTION99
2.55-2.620.31611470.20642552X-RAY DIFFRACTION100
2.62-2.70.28281260.20082563X-RAY DIFFRACTION100
2.7-2.780.23261440.20112587X-RAY DIFFRACTION100
2.78-2.880.24451420.19072575X-RAY DIFFRACTION100
2.88-30.26581440.20232555X-RAY DIFFRACTION100
3-3.140.29221310.19772604X-RAY DIFFRACTION100
3.14-3.30.2571440.20022584X-RAY DIFFRACTION100
3.3-3.510.24791430.18492583X-RAY DIFFRACTION100
3.51-3.780.24261370.15582623X-RAY DIFFRACTION100
3.78-4.160.16771590.13082603X-RAY DIFFRACTION100
4.16-4.760.17091360.12332644X-RAY DIFFRACTION100
4.76-5.980.17721500.14432647X-RAY DIFFRACTION100
5.99-100.20541510.16422789X-RAY DIFFRACTION100

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