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- PDB-6bfy: Crystal structure of enolase from Escherichia coli with bound 2-p... -

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Basic information

Entry
Database: PDB / ID: 6bfy
TitleCrystal structure of enolase from Escherichia coli with bound 2-phosphoglycerate substrate
ComponentsEnolase
KeywordsLYASE / Enolase / substrate / 2-phosphoglycerate / Escherichia coli
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
2-PHOSPHOGLYCERIC ACID / Enolase / Enolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsErlandsen, H. / Wright, D. / Krucinska, J.
CitationJournal: Biochemistry / Year: 2019
Title: Structural and Functional Studies of Bacterial Enolase, a Potential Target against Gram-Negative Pathogens.
Authors: Krucinska, J. / Falcone, E. / Erlandsen, H. / Hazeen, A. / Lombardo, M.N. / Estrada, A. / Robinson, V.L. / Anderson, A.C. / Wright, D.L.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2019Group: Data collection / 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 1.3Oct 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 / refine_hist / 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 / _refine_hist.d_res_low / _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
F: Enolase
D: Enolase
E: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,04049
Polymers284,2426
Non-polymers3,79843
Water19,8711103
1
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,17718
Polymers94,7472
Non-polymers1,43016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-191 kcal/mol
Surface area28770 Å2
MethodPISA
2
C: Enolase
D: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,98116
Polymers94,7472
Non-polymers1,23414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-147 kcal/mol
Surface area28770 Å2
MethodPISA
3
F: Enolase
E: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,88115
Polymers94,7472
Non-polymers1,13413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-136 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.940, 142.400, 206.640
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 ABCFDE

#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 (E. coli)
References: UniProt: B7MLA0, UniProt: P0A6P9*PLUS, phosphopyruvate hydratase

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Non-polymers , 5 types, 1146 molecules

#2: Chemical
ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1103 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.0 M ammonium sulfate, 0.1 M MES, pH 6.0, 0.1 M sodium/potassium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1949 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2017
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: 1.1949 Å / Relative weight: 1
ReflectionResolution: 1.81→78.61 Å / Num. obs: 283200 / % possible obs: 100 % / Redundancy: 4 % / Biso Wilson estimate: 17.49 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.062 / Rrim(I) all: 0.132 / Net I/σ(I): 6.1
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 13929 / CC1/2: 0.813 / Rpim(I) all: 0.349 / Rrim(I) all: 0.702 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FYM

2fym


Resolution: 1.81→78.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.101 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23223 14046 5 %RANDOM
Rwork0.16562 ---
obs0.16892 269041 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2--0.92 Å20 Å2
3----2.6 Å2
Refinement stepCycle: 1 / Resolution: 1.81→78.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19500 0 206 1103 20809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.01919934
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218946
X-RAY DIFFRACTIONr_angle_refined_deg2.2311.97826834
X-RAY DIFFRACTIONr_angle_other_deg1.18344087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91552627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85525.896804
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.479153574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4311572
X-RAY DIFFRACTIONr_chiral_restr0.1480.23035
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0222367
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023593
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_it3.5632.33510523
X-RAY DIFFRACTIONr_mcbond_other3.5622.33510522
X-RAY DIFFRACTIONr_mcangle_it3.9383.49413145
X-RAY DIFFRACTIONr_mcangle_other3.9383.49413146
X-RAY DIFFRACTIONr_scbond_it4.7632.8319411
X-RAY DIFFRACTIONr_scbond_other4.7582.839407
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1244.02613684
X-RAY DIFFRACTIONr_long_range_B_refined4.63128.94722156
X-RAY DIFFRACTIONr_long_range_B_other4.63128.94822157
X-RAY DIFFRACTIONr_rigid_bond_restr4.544338880
X-RAY DIFFRACTIONr_sphericity_free17.3395628
X-RAY DIFFRACTIONr_sphericity_bonded10.21539145
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 1018 -
Rwork0.274 19766 -
obs--99.77 %

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