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- PDB-4z17: Thermostable enolase from Chloroflexus aurantiacus -

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Basic information

Entry
Database: PDB / ID: 4z17
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 / 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
PHOSPHOENOLPYRUVATE / Enolase
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZadvornyy, O.A. / Peters, J.W.
Funding support United States, 3items
OrganizationGrant numberCountry
AFOSRFA9550-14-1-0147 United States
DURIPW911NF0510255 United States
National Aeronautic Space Administration (NASA, United States)NAG5-8807 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 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_nat / pdbx_audit_support ...entity_src_nat / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _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
Revision 1.2Sep 27, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_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)92,3258
Polymers91,8922
Non-polymers4336
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-4 kcal/mol
Surface area30320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.279, 146.279, 101.777
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9
Details: Bis-Tris propane buffer (0.1 M, pH 9.0), 0.21 M NaCl and 28% PEG 1500, 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: Apr 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.65→37.68 Å / Num. obs: 31118 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 64.47 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 3.2
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IYX
Resolution: 2.65→37.68 Å / Cor.coef. Fo:Fc: 0.9233 / Cor.coef. Fo:Fc free: 0.9012 / SU R Cruickshank DPI: 0.556 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.485 / SU Rfree Blow DPI: 0.275 / SU Rfree Cruickshank DPI: 0.286
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1556 5 %RANDOM
Rwork0.193 ---
obs0.1953 31114 99.56 %-
Displacement parametersBiso mean: 66.07 Å2
Baniso -1Baniso -2Baniso -3
1-6.8872 Å20 Å20 Å2
2--6.8872 Å20 Å2
3----13.7744 Å2
Refine analyzeLuzzati coordinate error obs: 0.331 Å
Refinement stepCycle: 1 / Resolution: 2.65→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6369 0 24 29 6422
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016484HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.168786HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2268SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes172HARMONIC2
X-RAY DIFFRACTIONt_gen_planes957HARMONIC5
X-RAY DIFFRACTIONt_it6484HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion19.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion857SEMIHARMONIC5
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_contact7636SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.74 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3092 147 5.19 %
Rwork0.2187 2687 -
all0.223 2834 -
obs--99.56 %

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