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- PDB-5o34: ThnE from S.clavuligerus -

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Basic information

Entry
Database: PDB / ID: 5o34
TitleThnE from S.clavuligerus
ComponentsEnoyl-CoA hydratase carB homologue
KeywordsLYASE / Antibiotics / thienamycin biosynthesis
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1610 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA hydratase carB homologue
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsValegard, K. / Andersson, I.
CitationJournal: To Be Published
Title: Structure of ThnE from the thienamycin biosynthesis.
Authors: Valegard, K.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase carB homologue
B: Enoyl-CoA hydratase carB homologue
C: Enoyl-CoA hydratase carB homologue


Theoretical massNumber of molelcules
Total (without water)96,9983
Polymers96,9983
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-26 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.220, 113.220, 158.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Enoyl-CoA hydratase carB homologue


Mass: 32332.582 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q83XP9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.81 Å3/Da / Density % sol: 67.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M citric acid pH 5.5, 1.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→44.02 Å / Num. obs: 71350 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 65.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.36
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.034 / Num. unique obs: 5065 / CC1/2: 0.49 / % possible all: 94.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A7K

2a7k


Resolution: 2.45→44.02 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.918 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.252 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1907 5 %RANDOM
Rwork0.213 ---
obs0.214 38137 99.1 %-
Displacement parametersBiso mean: 64.58 Å2
Baniso -1Baniso -2Baniso -3
1--5.7632 Å20 Å20 Å2
2---5.7632 Å20 Å2
3---11.5264 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.45→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 0 7 4668
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094722HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.026371HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1680SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes709HARMONIC5
X-RAY DIFFRACTIONt_it4722HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion17.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion625SEMIHARMONIC5
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_contact5141SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.256 145 4.98 %
Rwork0.24 2764 -
all0.241 2909 -
obs--98.68 %

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