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- PDB-4mks: Crystal structure of enolase from Lactobacillus gasseri -

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Basic information

Entry
Database: PDB / ID: 4mks
TitleCrystal structure of enolase from Lactobacillus gasseri
ComponentsEnolase 2
KeywordsLYASE / enolase
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / magnesium ion binding / cell surface / extracellular region
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
Biological speciesLactobacillus gasseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.079 Å
AuthorsRaghunathan, K. / Harris, P.T. / Spurbeck, R.R. / Arvidson, C.G. / Arvidson, D.N.
CitationJournal: Febs Lett. / Year: 2014
Title: Crystal structure of an efficacious gonococcal adherence inhibitor: An enolase from Lactobacillus gasseri.
Authors: Raghunathan, K. / Harris, P.T. / Spurbeck, R.R. / Arvidson, C.G. / Arvidson, D.N.
History
DepositionSep 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / struct_site
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.ptnr1_label_seq_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.ptnr3_label_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enolase 2
B: Enolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0875
Polymers96,0032
Non-polymers843
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-39 kcal/mol
Surface area26690 Å2
MethodPISA
2
A: Enolase 2
B: Enolase 2
hetero molecules

A: Enolase 2
B: Enolase 2
hetero molecules

A: Enolase 2
B: Enolase 2
hetero molecules

A: Enolase 2
B: Enolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)384,34820
Polymers384,0128
Non-polymers33612
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area23150 Å2
ΔGint-187 kcal/mol
Surface area97250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.240, 145.240, 99.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 48001.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus gasseri (bacteria) / Strain: DSM 20243 / Gene: eno2, LGAS_1305 / Production host: Escherichia coli (E. coli) / References: UniProt: Q042F4, phosphopyruvate hydratase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 55.15 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9
Details: pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.079→54.45 Å / Num. obs: 62294

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Processing

Software
NameVersionClassification
HKL-2000data collection
ARP/wARPmodel building
PHENIXAutobuildmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXAutobuildphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISSMODEL generated using 1w6t template

1w6t


Resolution: 2.079→54.45 Å / SU ML: 0.15 / σ(F): 1.38 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 3155 5.06 %RANDOM
Rwork0.1891 ---
obs0.1914 62294 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.079→54.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 3 569 6614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036132
X-RAY DIFFRACTIONf_angle_d0.7638305
X-RAY DIFFRACTIONf_dihedral_angle_d13.5492233
X-RAY DIFFRACTIONf_chiral_restr0.052952
X-RAY DIFFRACTIONf_plane_restr0.0021097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.079-2.11010.29231410.25462529X-RAY DIFFRACTION100
2.1101-2.1430.26881500.23482510X-RAY DIFFRACTION100
2.143-2.17820.27231330.21752588X-RAY DIFFRACTION100
2.1782-2.21570.261520.20752535X-RAY DIFFRACTION100
2.2157-2.2560.2311340.20242570X-RAY DIFFRACTION100
2.256-2.29940.26391430.20522543X-RAY DIFFRACTION100
2.2994-2.34640.26951360.20022576X-RAY DIFFRACTION100
2.3464-2.39740.24241320.19972563X-RAY DIFFRACTION100
2.3974-2.45310.26741500.20122552X-RAY DIFFRACTION100
2.4531-2.51450.24791340.19732568X-RAY DIFFRACTION100
2.5145-2.58250.2721300.19082593X-RAY DIFFRACTION100
2.5825-2.65850.26161200.19352571X-RAY DIFFRACTION100
2.6585-2.74430.22481320.19712577X-RAY DIFFRACTION100
2.7443-2.84230.24451130.18742604X-RAY DIFFRACTION100
2.8423-2.95610.23491500.19562535X-RAY DIFFRACTION100
2.9561-3.09070.2581340.19792607X-RAY DIFFRACTION100
3.0907-3.25360.23991380.19542557X-RAY DIFFRACTION100
3.2536-3.45740.25551400.18552583X-RAY DIFFRACTION100
3.4574-3.72430.24751270.17182567X-RAY DIFFRACTION100
3.7243-4.0990.19171500.16172597X-RAY DIFFRACTION100
4.099-4.69180.19111530.15412545X-RAY DIFFRACTION100
4.6918-5.91010.19721350.17732608X-RAY DIFFRACTION100
5.9101-54.450.23681280.21272661X-RAY DIFFRACTION100

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