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- PDB-5wro: Crystal structure of Drosophila enolase -

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Basic information

Entry
Database: PDB / ID: 5wro
TitleCrystal structure of Drosophila enolase
ComponentsEnolase
KeywordsLYASE / enolase / hydrolyase / metabolism
Function / homology
Function and homology information


Glycolysis / Gluconeogenesis / regulation of vacuole fusion, non-autophagic / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / glucose homeostasis / magnesium ion binding / plasma membrane / cytoplasm
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
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.015 Å
AuthorsZhang, Z. / Shi, Z.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of enolase from Drosophila melanogaster.
Authors: Sun, C. / Xu, B. / Liu, X. / Zhang, Z. / Su, Z.
History
DepositionDec 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0339
Polymers47,3381
Non-polymers6968
Water5,999333
1
A: Enolase
hetero molecules

A: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,06618
Polymers94,6752
Non-polymers1,39116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area6920 Å2
ΔGint-144 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.820, 118.820, 229.792
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 47337.664 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 69-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Eno, CG17654 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus / References: UniProt: P15007, phosphopyruvate hydratase

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Non-polymers , 6 types, 341 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 10 mM CoCl2, 0.1 M CdCl2, 0.1 M MES pH6.5, 1.9 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.015→50 Å / Num. obs: 41492 / % possible obs: 98 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B97

3b97


Resolution: 2.015→38.327 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 4052 5.07 %
Rwork0.1591 --
obs0.1611 41492 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.015→38.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 26 333 3628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073394
X-RAY DIFFRACTIONf_angle_d0.8024602
X-RAY DIFFRACTIONf_dihedral_angle_d4.6192750
X-RAY DIFFRACTIONf_chiral_restr0.05522
X-RAY DIFFRACTIONf_plane_restr0.004602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.015-2.03870.30071270.27362617X-RAY DIFFRACTION100
2.0387-2.06360.3021290.25792566X-RAY DIFFRACTION100
2.0636-2.08970.28741090.23722672X-RAY DIFFRACTION100
2.0897-2.11720.24791500.2232597X-RAY DIFFRACTION100
2.1172-2.14620.26341180.20722639X-RAY DIFFRACTION100
2.1462-2.17680.2431560.20582598X-RAY DIFFRACTION100
2.1768-2.20930.25411280.19812666X-RAY DIFFRACTION100
2.2093-2.24380.21791290.19982609X-RAY DIFFRACTION100
2.2438-2.28060.22931660.1912606X-RAY DIFFRACTION100
2.2806-2.320.21781610.17582556X-RAY DIFFRACTION100
2.32-2.36210.21511640.17292596X-RAY DIFFRACTION100
2.3621-2.40760.23231600.17672596X-RAY DIFFRACTION100
2.4076-2.45670.21081630.17372600X-RAY DIFFRACTION100
2.4567-2.51010.20761350.17612639X-RAY DIFFRACTION100
2.5101-2.56850.21481220.17112612X-RAY DIFFRACTION100
2.5685-2.63270.20081810.15392601X-RAY DIFFRACTION100
2.6327-2.70390.17891450.15352627X-RAY DIFFRACTION100
2.7039-2.78340.21511110.1592624X-RAY DIFFRACTION100
2.7834-2.87320.22631510.15622582X-RAY DIFFRACTION100
2.8732-2.97590.18621420.16112622X-RAY DIFFRACTION100
2.9759-3.0950.18431290.15672630X-RAY DIFFRACTION100
3.095-3.23580.1981320.15942635X-RAY DIFFRACTION100
3.2358-3.40630.19461360.14782609X-RAY DIFFRACTION100
3.4063-3.61950.20231440.13962595X-RAY DIFFRACTION100
3.6195-3.89870.16411410.13132626X-RAY DIFFRACTION100
3.8987-4.29060.17451400.12512647X-RAY DIFFRACTION100
4.2906-4.91040.18841080.12362659X-RAY DIFFRACTION100
4.9104-6.18240.16351350.14792602X-RAY DIFFRACTION100
6.1824-38.33350.18591400.17262612X-RAY DIFFRACTION99
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)
12.11730.52830.98343.1683-0.64092.7471-0.14360.05730.3091-0.01330.0125-0.1188-0.30780.19320.07840.1871-0.0608-0.02620.2131-0.00310.2916-16.177262.2082-0.4058
21.48650.21370.11751.87360.20751.3383-0.06690.4149-0.0536-0.3870.0399-0.22070.06740.23980.03310.2529-0.0330.0270.3169-0.01470.1898-18.933443.0852-17.3066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 62 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 500 )

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