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- PDB-6npf: Structure of E.coli enolase in complex with an analog of the natu... -

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Basic information

Entry
Database: PDB / ID: 6npf
TitleStructure of E.coli enolase in complex with an analog of the natural product SF-2312 metabolite.
ComponentsEnolase
KeywordsLYASE / Natural inhibitor / complex / enolase / SF2312
Function / homology
Function and homology information


bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / magnesium ion binding / cell surface ...bacterial degradosome / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / RNA catabolic process / RNA processing / glycolytic process / cytoskeleton / magnesium ion binding / cell surface / 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-KVM / L(+)-TARTARIC ACID / Enolase / Enolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsErlandsen, H. / Krucinska, J. / Lombardo, M. / Wright, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI140734-01 United States
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
DepositionJan 17, 2019Deposition 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 11, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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
B: Enolase
C: Enolase
D: Enolase
F: Enolase
E: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,84833
Polymers284,2426
Non-polymers2,60627
Water4,486249
1
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,56911
Polymers94,7472
Non-polymers8219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-66 kcal/mol
Surface area28710 Å2
MethodPISA
2
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,80613
Polymers94,7472
Non-polymers1,05811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-101 kcal/mol
Surface area29140 Å2
MethodPISA
3
F: Enolase
E: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4749
Polymers94,7472
Non-polymers7277
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-61 kcal/mol
Surface area29800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.180, 143.110, 206.679
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDFE

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


Mass: 47373.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eno, ECS88_3047 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: B7MLA0, UniProt: P0A6P9*PLUS, phosphopyruvate hydratase

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Non-polymers , 6 types, 276 molecules

#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-KVM / [(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]phosphonic acid


Mass: 195.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6NO6P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.1 M Ammonium Sulfate, 0.1 M MES buffer pH 6.0, 0.2 M Sodium/Potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 10, 2018
Details: Mirror: Flat bent collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 2.57→93.03 Å / Num. obs: 97620 / % possible obs: 99.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 35.5 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.075 / Rrim(I) all: 0.106 / Net I/σ(I): 5.9
Reflection shellResolution: 2.57→2.62 Å / Redundancy: 2 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4421 / CC1/2: 0.791 / Rpim(I) all: 0.396 / Rrim(I) all: 0.56 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D3Q

6d3q


Resolution: 2.57→93.03 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.895 / SU B: 14.999 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.599 / ESU R Free: 0.311 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25646 4924 5 %RANDOM
Rwork0.19052 ---
obs0.19383 92667 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.153 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å20 Å2
2--1.6 Å20 Å2
3----5.28 Å2
Refinement stepCycle: 1 / Resolution: 2.57→93.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19325 0 151 249 19725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01319691
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718813
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.63826484
X-RAY DIFFRACTIONr_angle_other_deg1.2291.58443772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56252589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29524.56864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.858153552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7971572
X-RAY DIFFRACTIONr_chiral_restr0.0630.22656
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023619
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5354.93110401
X-RAY DIFFRACTIONr_mcbond_other3.5354.93110400
X-RAY DIFFRACTIONr_mcangle_it5.3517.38412975
X-RAY DIFFRACTIONr_mcangle_other5.3517.38512976
X-RAY DIFFRACTIONr_scbond_it3.595.2699290
X-RAY DIFFRACTIONr_scbond_other3.595.279291
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5367.75113510
X-RAY DIFFRACTIONr_long_range_B_refined7.72858.18621206
X-RAY DIFFRACTIONr_long_range_B_other7.72858.18721207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.574→2.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 337 -
Rwork0.375 6421 -
obs--93.84 %

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