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- PDB-6e55: 1.57 Angstroem Crystal Structure of FeoA from Klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 6.0E+55
Title1.57 Angstroem Crystal Structure of FeoA from Klebsiella pneumoniae
ComponentsFeoA protein
KeywordsTRANSPORT PROTEIN / Iron Transport / Protein-Protein Interactions / Protein Regulation
Function / homology
Function and homology information


transition metal ion binding
Similarity search - Function
: / FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / Transcriptional repressor, C-terminal / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Ferrous iron transport protein A / Fe(2+) transport protein A
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å
AuthorsLinkous, R.O. / Sestok, A.E. / Smith, A.T.
CitationJournal: Proteins / Year: 2019
Title: The crystal structure of Klebsiella pneumoniae FeoA reveals a site for protein-protein interactions.
Authors: Linkous, R.O. / Sestok, A.E. / Smith, A.T.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: FeoA protein
B: FeoA protein
C: FeoA protein
D: FeoA protein
E: FeoA protein
F: FeoA protein


Theoretical massNumber of molelcules
Total (without water)61,9436
Polymers61,9436
Non-polymers00
Water13,097727
1
A: FeoA protein


Theoretical massNumber of molelcules
Total (without water)10,3241
Polymers10,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FeoA protein


Theoretical massNumber of molelcules
Total (without water)10,3241
Polymers10,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FeoA protein


Theoretical massNumber of molelcules
Total (without water)10,3241
Polymers10,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FeoA protein


Theoretical massNumber of molelcules
Total (without water)10,3241
Polymers10,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: FeoA protein


Theoretical massNumber of molelcules
Total (without water)10,3241
Polymers10,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: FeoA protein


Theoretical massNumber of molelcules
Total (without water)10,3241
Polymers10,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.010, 79.010, 74.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
FeoA protein / Ferrous iron transport protein A / Ferrous iron transporter A


Mass: 10323.873 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: feoA / Production host: Escherichia coli (E. coli) / References: UniProt: W9BB34, UniProt: A6TF31*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 2.0 M ammonium sulfate, 0.1 M ammonium fluoride, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.255
11K, H, -L20.244
11-K, -H, -L30.25
11-h,-k,l40.251
ReflectionResolution: 1.57→37.33 Å / Num. obs: 72562 / % possible obs: 99.19 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.7
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7267 / CC1/2: 0.469 / % possible all: 99.45

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→31.1 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.927 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.019 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 -5.2 %RANDOM
Rwork0.1742 ---
obs-72465 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.79 Å2
Baniso -1Baniso -2Baniso -3
1-5.56 Å20 Å20 Å2
2--5.56 Å20 Å2
3----11.12 Å2
Refinement stepCycle: 1 / Resolution: 1.57→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 0 727 4543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0143900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173678
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.6495274
X-RAY DIFFRACTIONr_angle_other_deg0.7551.6258604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.325474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01420198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61315690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6541536
X-RAY DIFFRACTIONr_chiral_restr0.050.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.6 Å
RfactorNum. reflection% reflection
Rfree0.1691 3765 -
Rwork0.1514 7267 -
obs--99.45 %

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