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- PDB-4z1y: Thermostable enolase from Chloroflexus aurantiacus with substrate... -

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Basic information

Entry
Database: PDB / ID: 4z1y
TitleThermostable enolase from Chloroflexus aurantiacus with substrate 2-phosphoglycerate
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
2-PHOSPHOGLYCERIC ACID / Enolase
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsZadvornyy, O.A. / Peters, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
AFOSR 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 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_nat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
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_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enolase
B: Enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3126
Polymers91,8922
Non-polymers4214
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-2 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.324, 146.324, 101.883
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: Chemical ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9
Details: 0.1 M Bis-Tris propane buffer (pH 9.0), 0.21 M NaCl, 28% (w/v) PEG 1500 and 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95369 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.53→37.7 Å / Num. obs: 35899 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 61.48 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.8
Reflection shellResolution: 2.53→2.67 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.6 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→37.7 Å / Cor.coef. Fo:Fc: 0.9281 / Cor.coef. Fo:Fc free: 0.9016 / SU R Cruickshank DPI: 0.429 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.388 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.27
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 1794 5 %RANDOM
Rwork0.2136 ---
obs0.2155 35894 99.92 %-
Displacement parametersBiso mean: 62.96 Å2
Baniso -1Baniso -2Baniso -3
1-4.0153 Å20 Å20 Å2
2--4.0153 Å20 Å2
3----8.0307 Å2
Refine analyzeLuzzati coordinate error obs: 0.363 Å
Refinement stepCycle: 1 / Resolution: 2.53→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6383 0 24 23 6430
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016501HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.28820HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2258SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes964HARMONIC5
X-RAY DIFFRACTIONt_it6501HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion19.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion873SEMIHARMONIC5
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_contact7785SEMIHARMONIC4
LS refinement shellResolution: 2.53→2.6 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2928 143 4.89 %
Rwork0.2351 2781 -
all0.2379 2924 -
obs--99.92 %

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