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- PDB-6d3q: Crystal structure of Escherichia coli enolase complexed with a na... -

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Basic information

Entry
Database: PDB / ID: 6d3q
TitleCrystal structure of Escherichia coli enolase complexed with a natural inhibitor SF2312.
ComponentsEnolase
KeywordsLYASE/LYASE inhibitor / Enolase / complex / natural inhibitor / SF2312 / LYASE / LYASE-LYASE inhibitor complex
Function / homology
Function and homology information


bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / cell surface / magnesium ion binding ...bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / identical protein binding / 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 / Enolase / Enolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsErlandsen, H. / Krucinska, J. / Hazeen, A. / Wright, D.
CitationJournal: Sci Rep / Year: 2019
Title: Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate.
Authors: Krucinska, J. / Lombardo, M.N. / Erlandsen, H. / Hazeen, A. / Duay, S.S. / Pattis, J.G. / Robinson, V.L. / May, E.R. / Wright, D.L.
History
DepositionApr 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enolase
C: Enolase
B: Enolase
E: Enolase
F: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,82141
Polymers278,7346
Non-polymers3,08735
Water9,368520
1
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,77912
Polymers92,9112
Non-polymers86810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-90 kcal/mol
Surface area29160 Å2
MethodPISA
2
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,97514
Polymers92,9112
Non-polymers1,06412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-98 kcal/mol
Surface area29420 Å2
MethodPISA
3
E: Enolase
F: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,06715
Polymers92,9112
Non-polymers1,15613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-113 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.751, 142.071, 207.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ACBEFD

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


Mass: 46455.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eno / Production host: Escherichia coli (E. coli)
References: UniProt: B7MLA0, UniProt: P0A6P9*PLUS, phosphopyruvate hydratase

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Non-polymers , 5 types, 555 molecules

#2: Chemical
ChemComp-4NG / [(3S,5S)-1,5-dihydroxy-2-oxopyrrolidin-3-yl]phosphonic acid


Mass: 197.083 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.3 M Ammonium Sulfate, 0.2 M Na/K tartrate, 0.1M Mes pH 6.0 and 2 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2017
Details: Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.24→207.28 Å / Num. obs: 147731 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.098 / Rrim(I) all: 0.25 / Net I/σ(I): 4.6
Reflection shellResolution: 2.24→2.34 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.444 / Num. unique obs: 17855 / CC1/2: 0.958 / Rpim(I) all: 0.142 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BFY

6bfy


Resolution: 2.24→207.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.348 / SU ML: 0.132 / SU R Cruickshank DPI: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.187
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 7420 5 %RANDOM
Rwork0.163 ---
obs0.1657 140311 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.57 Å2 / Biso mean: 38.102 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å20 Å2
2--1.35 Å20 Å2
3----3.38 Å2
Refinement stepCycle: final / Resolution: 2.24→207.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19500 0 174 520 20194
Biso mean--47.68 32.04 -
Num. residues----2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01919896
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218938
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.97426786
X-RAY DIFFRACTIONr_angle_other_deg1.0742.99844069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65652623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.65625.778810
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.177153566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0471572
X-RAY DIFFRACTIONr_chiral_restr0.1110.23031
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222363
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023589
LS refinement shellResolution: 2.244→2.302 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 518 -
Rwork0.219 10318 -
all-10836 -
obs--99.66 %

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