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- PDB-4zcw: Structure of Human Enolase 2 in complex with SF2312 -

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Basic information

Entry
Database: PDB / ID: 4zcw
TitleStructure of Human Enolase 2 in complex with SF2312
ComponentsGamma-enolase
KeywordsLYASE/LYASE INHIBITOR / enolase gamma / glycolysis / neuron specific enolase / inhibitor / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / gluconeogenesis / glycolytic process / perikaryon ...phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / photoreceptor inner segment / gluconeogenesis / glycolytic process / perikaryon / magnesium ion binding / extracellular space / extracellular exosome / membrane / plasma 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 / Gamma-enolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.992 Å
AuthorsLeonard, P.G. / Maxwell, D. / Czako, B. / Muller, F.L.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: SF2312 is a natural phosphonate inhibitor of enolase.
Authors: Leonard, P.G. / Satani, N. / Maxwell, D. / Lin, Y.H. / Hammoudi, N. / Peng, Z. / Pisaneschi, F. / Link, T.M. / Lee, G.R. / Sun, D. / Prasad, B.A. / Di Francesco, M.E. / Czako, B. / Asara, J. ...Authors: Leonard, P.G. / Satani, N. / Maxwell, D. / Lin, Y.H. / Hammoudi, N. / Peng, Z. / Pisaneschi, F. / Link, T.M. / Lee, G.R. / Sun, D. / Prasad, B.A. / Di Francesco, M.E. / Czako, B. / Asara, J.M. / Wang, Y.A. / Bornmann, W. / DePinho, R.A. / Muller, F.L.
History
DepositionApr 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Nov 23, 2016Group: Database references
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-enolase
B: Gamma-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7908
Polymers96,2992
Non-polymers4916
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-46 kcal/mol
Surface area29000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 109.460, 117.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 434 / Label seq-ID: 2 - 434

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Gamma-enolase / 2-phospho-D-glycerate hydro-lyase / Enolase 2 / Neural enolase / Neuron-specific enolase / NSE


Mass: 48149.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENO2 / Plasmid: pJL-H6 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Rosetta2 plysS / References: UniProt: P09104, phosphopyruvate hydratase
#2: Chemical ChemComp-4NG / [(3S,5S)-1,5-dihydroxy-2-oxopyrrolidin-3-yl]phosphonic acid


Mass: 197.083 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8NO6P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, pH 6.5, 200 mM ammonium acetate, 18-22% w/v PEG3350, overnight crystal soak in 4 mM SF2312, 100 mM Bis-Tris, 200 mM ammonium acetate, 32% w/v PEG3350, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2014
RadiationMonochromator: Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.99→80.02 Å / Num. obs: 60867 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 21.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Net I/σ(I): 13.3 / Num. measured all: 428996 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.99-2.046.60.4493.82884443990.9060.18999.6
8.91-80.026.40.03126.850637850.9990.01399.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.95 Å51.69 Å
Translation5.95 Å51.69 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX1.9-1692refinement
Coot0.7.1model building
PDB_EXTRACT3.15data extraction
iMOSFLM7.1.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UCC chain A

3ucc


Resolution: 1.992→51.686 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 3064 5.04 %Random selection
Rwork0.1567 57724 --
obs0.159 60788 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.16 Å2 / Biso mean: 25.1923 Å2 / Biso min: 5.64 Å2
Refinement stepCycle: final / Resolution: 1.992→51.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 28 595 7251
Biso mean--18.75 32.5 -
Num. residues----866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0186792
X-RAY DIFFRACTIONf_angle_d1.3969201
X-RAY DIFFRACTIONf_chiral_restr0.0921035
X-RAY DIFFRACTIONf_plane_restr0.0081211
X-RAY DIFFRACTIONf_dihedral_angle_d13.8012527
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3929X-RAY DIFFRACTION5.262TORSIONAL
12B3929X-RAY DIFFRACTION5.262TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.992-2.02320.30921320.22322570270299
2.0232-2.05630.25561320.191126042736100
2.0563-2.09180.23791370.185225642701100
2.0918-2.12980.25741310.172926252756100
2.1298-2.17080.26821450.179525562701100
2.1708-2.21510.22161490.170326042753100
2.2151-2.26330.20091540.165125882742100
2.2633-2.31590.21971260.161425822708100
2.3159-2.37390.22411240.161126092733100
2.3739-2.4380.21171330.160526502783100
2.438-2.50980.21681620.155525512713100
2.5098-2.59080.18661450.157826002745100
2.5908-2.68340.21591450.157226172762100
2.6834-2.79080.20871490.157625822731100
2.7908-2.91780.21471650.160926092774100
2.9178-3.07160.21351170.165326572774100
3.0716-3.2640.22581500.169326202770100
3.264-3.5160.1981110.158426682779100
3.516-3.86970.18131340.145626612795100
3.8697-4.42940.14111160.128926942810100
4.4294-5.57960.16411570.13326952852100
5.5796-51.70380.18251500.151228182968100

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