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- PDB-5eep: Crystal structure of E. coli CsdE -

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Basic information

Entry
Database: PDB / ID: 5eep
TitleCrystal structure of E. coli CsdE
ComponentsCsdA-binding activator
KeywordsLIGASE / sulfur-accepting protein / SufE superfamily / CsdA interaction / sulfur utilization
Function / homology
Function and homology information


cyclic threonylcarbamoyladenosine biosynthetic process / sulfur carrier activity
Similarity search - Function
Cysteine desulfurase, sulphur acceptor subunit CsdE / Fe-S metabolism associated domain, SufE-like / Fe-S metabolism associated domain / Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cysteine desulfurase sulfur acceptor subunit CsdE / Sulfur acceptor protein CsdE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsPark, S.Y.
CitationJournal: Int.J.Biol.Macromol. / Year: 2016
Title: The crystal structure of Escherichia coli CsdE
Authors: Kenne, A.N. / Kim, S. / Park, S.Y.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CsdA-binding activator


Theoretical massNumber of molelcules
Total (without water)16,2081
Polymers16,2081
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7440 Å2
Unit cell
Length a, b, c (Å)43.521, 43.521, 145.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

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Components

#1: Protein CsdA-binding activator / Sulfur acceptor protein CsdE


Mass: 16208.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECONIH1_16050, SK78_01951 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1ADS4, UniProt: P0AGF2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.2M sodium acetate, 0.1M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 5950 / % possible obs: 99.8 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 55.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 10.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementResolution: 2.4→41.69 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.559 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28495 273 4.6 %RANDOM
Rwork0.22852 ---
obs0.23127 5723 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.757 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å20 Å2
2---0.45 Å20 Å2
3---0.9 Å2
Refinement stepCycle: 1 / Resolution: 2.4→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 0 40 1104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191081
X-RAY DIFFRACTIONr_bond_other_d0.0010.021068
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9721463
X-RAY DIFFRACTIONr_angle_other_deg0.79332449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55224.56546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19915187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.488157
X-RAY DIFFRACTIONr_chiral_restr0.0720.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4073.852559
X-RAY DIFFRACTIONr_mcbond_other2.4033.849558
X-RAY DIFFRACTIONr_mcangle_it4.0845.77697
X-RAY DIFFRACTIONr_mcangle_other4.0825.774698
X-RAY DIFFRACTIONr_scbond_it2.3824.097522
X-RAY DIFFRACTIONr_scbond_other2.384.101523
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9686.014767
X-RAY DIFFRACTIONr_long_range_B_refined7.97630.5461239
X-RAY DIFFRACTIONr_long_range_B_other7.78530.3331222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 18 -
Rwork0.35 409 -
obs--99.77 %
Refinement TLS params.Method: refined / Origin x: 2.0093 Å / Origin y: 13.0571 Å / Origin z: 45.8476 Å
111213212223313233
T0.1565 Å2-0.0115 Å20.0109 Å2-0.1717 Å2-0.0016 Å2--0.0227 Å2
L2.6193 °2-1.6816 °20.2367 °2-6.6805 °2-1.4341 °2--2.6427 °2
S-0.0458 Å °-0.423 Å °0.1513 Å °0.7287 Å °-0.0653 Å °-0.0797 Å °-0.334 Å °0.0933 Å °0.1111 Å °

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