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- PDB-4yws: Thermostable enolase from Chloroflexus aurantiacus -

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Basic information

Entry
Database: PDB / ID: 4yws
TitleThermostable enolase from Chloroflexus aurantiacus
ComponentsEnolase
KeywordsLYASE / enolase / thermostability / thermophilic origin / phylogeny
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / cell surface / magnesium ion binding / 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 speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZadvornyy, O.A. / Peters, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
AFOSRFA9550-14-1-0147 United States
CitationJournal: Front Bioeng Biotechnol / Year: 2015
Title: Biochemical and Structural Characterization of Enolase from Chloroflexus aurantiacus: Evidence for a Thermophilic Origin.
Authors: Zadvornyy, O.A. / Boyd, E.S. / Posewitz, M.C. / Zorin, N.A. / Peters, J.W.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_nat / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9404
Polymers91,8922
Non-polymers492
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-2 kcal/mol
Surface area30750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.319, 146.319, 102.989
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-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 45945.863 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
Strain: ATCC 29366 / DSM 635 / J-10-fl / References: UniProt: A9WCM4, phosphopyruvate hydratase
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.01 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Bis-Tris propane buffer (pH 9.0), 0.21 M NaCl and 28% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.45→103.5 Å / Num. obs: 39821 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 56.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 27.9
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 4.4 / % possible all: 98.2

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IYX

1iyx


Resolution: 2.45→37.76 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.292 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.232
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2015 5.06 %RANDOM
Rwork0.199 ---
obs0.201 39821 99.7 %-
Displacement parametersBiso mean: 65.06 Å2
Baniso -1Baniso -2Baniso -3
1-7.4919 Å20 Å20 Å2
2--7.4919 Å20 Å2
3----14.9838 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.45→37.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6057 0 2 95 6154
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016179HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.128352HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2145SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes164HARMONIC2
X-RAY DIFFRACTIONt_gen_planes893HARMONIC5
X-RAY DIFFRACTIONt_it6179HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion19.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion820SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7162SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2424 132 4.68 %
Rwork0.2262 2691 -
all0.227 2823 -
obs--99.68 %

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