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- PDB-6bfz: Crystal structure of enolase from E. coli with a mixture of apo f... -

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Basic information

Entry
Database: PDB / ID: 6bfz
TitleCrystal structure of enolase from E. coli with a mixture of apo form, substrate, and product form
ComponentsEnolase
KeywordsLYASE / Enolase / Escherichia coli / Apo / substrate / product
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
2-PHOSPHOGLYCERIC ACID / PHOSPHOENOLPYRUVATE / Enolase / Enolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)287,21635
Polymers284,2426
Non-polymers2,97429
Water12,178676
1
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,46411
Polymers94,7472
Non-polymers7179
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-110 kcal/mol
Surface area30090 Å2
MethodPISA
2
E: Enolase
F: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,00813
Polymers94,7472
Non-polymers1,26011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-98 kcal/mol
Surface area29070 Å2
MethodPISA
3
D: Enolase
C: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,74411
Polymers94,7472
Non-polymers9969
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-82 kcal/mol
Surface area29440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.262, 143.293, 207.040
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 ABEFDC

#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 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B7MLA0, UniProt: P0A6P9*PLUS, phosphopyruvate hydratase

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Non-polymers , 7 types, 705 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#6: Chemical
ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O7P
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979186 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2017
Details: White beam slits, double crystal Si(111) monochromator with horizontal theta-axis, tandem flat beam deflecting silicon mirrors (Pd and Si lanes), Kirkpatrick-Baez focusing silica mirrors, Pd- ...Details: White beam slits, double crystal Si(111) monochromator with horizontal theta-axis, tandem flat beam deflecting silicon mirrors (Pd and Si lanes), Kirkpatrick-Baez focusing silica mirrors, Pd-coated, each bent adaptively with 16 piezo actuators
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979186 Å / Relative weight: 1
ReflectionResolution: 2.21→29.69 Å / Num. obs: 165432 / % possible obs: 99.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.036 / Rrim(I) all: 0.051 / Net I/σ(I): 13.8
Reflection shellResolution: 2.21→2.24 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7139 / CC1/2: 0.786 / Rpim(I) all: 0.332 / Rrim(I) all: 0.47 / % possible all: 87.4

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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: 2.21→29.69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.078 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 8374 5.1 %RANDOM
Rwork0.17148 ---
obs0.17384 156961 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--2.12 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.21→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19431 0 167 676 20274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01919833
X-RAY DIFFRACTIONr_bond_other_d0.0020.0218882
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.97726694
X-RAY DIFFRACTIONr_angle_other_deg1.07343929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00352616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.41625.893801
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.741153549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0671572
X-RAY DIFFRACTIONr_chiral_restr0.1120.23022
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222269
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023581
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_it3.373.80110485
X-RAY DIFFRACTIONr_mcbond_other3.3683.810484
X-RAY DIFFRACTIONr_mcangle_it4.6175.6813091
X-RAY DIFFRACTIONr_mcangle_other4.6175.6813092
X-RAY DIFFRACTIONr_scbond_it4.5084.2979348
X-RAY DIFFRACTIONr_scbond_other4.5084.2979348
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5226.2113603
X-RAY DIFFRACTIONr_long_range_B_refined7.69745.44821822
X-RAY DIFFRACTIONr_long_range_B_other7.70245.39621722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 597 -
Rwork0.26 10536 -
obs--91.32 %

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