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- PDB-8vv6: The crystal structure of Brucella abortus FtrA-H151A mutant -

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Basic information

Entry
Database: PDB / ID: 8vv6
TitleThe crystal structure of Brucella abortus FtrA-H151A mutant
ComponentsFtrA
KeywordsMETAL BINDING PROTEIN / Brucella abortus / iron transport / FtrABCD
Function / homologyPeriplasmic metal-binding protein Tp34-type / Periplasmic metal-binding protein Tp34-type superfamily / Fe2+ transport protein / UPF0423 protein BRA0381/BS1330_II0378
Function and homology information
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsRoy, S. / Garcia, B.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structures of FtrA and FtrB of the Brucella abortus ferrous iron transporter FtrABCD system
Authors: Roy, S. / Kerkan, A. / Martin, D.W. / Banerjee, S. / Garcia, B.L.
History
DepositionJan 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FtrA
B: FtrA
C: FtrA
D: FtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7356
Polymers69,5514
Non-polymers1842
Water11,061614
1
A: FtrA
B: FtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8683
Polymers34,7752
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-22 kcal/mol
Surface area13850 Å2
MethodPISA
2
C: FtrA
D: FtrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8683
Polymers34,7752
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-21 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.158, 57.675, 101.027
Angle α, β, γ (deg.)90.000, 130.100, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-330-

HOH

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Components

#1: Protein
FtrA / UPF0423 protein BRA0381/BS1330_II0378


Mass: 17387.709 Da / Num. of mol.: 4 / Mutation: H151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Gene: BRA0381, BS1330_II0378 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8FWR4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→36.53 Å / Num. obs: 89988 / % possible obs: 98.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 19.86 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.044 / Rrim(I) all: 0.107 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Num. unique obsCC1/2Rpim(I) allRrim(I) allDiffraction-IDMean I/σ(I) obs
3.34-36.5391790.9960.0290.0721
2.65-3.3491700.9940.0370.0921
2.32-2.6588830.9880.0480.1131
2.1-2.3290610.9860.0570.1371
1.95-2.190760.980.0960.2251
1.84-1.9589480.9750.1020.251
1.75-1.8488490.9510.1490.351
1.67-1.7589690.9250.2340.5721
1.61-1.6789090.8660.3230.7741
1.55-1.6189440.7820.380.85812.32

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5I0V

5i0v


Resolution: 1.55→36.53 Å / SU ML: 0.1713 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1904 2009 2.23 %
Rwork0.1728 87907 -
obs0.1732 89916 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 1.55→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 12 614 5271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554791
X-RAY DIFFRACTIONf_angle_d0.81346500
X-RAY DIFFRACTIONf_chiral_restr0.0538665
X-RAY DIFFRACTIONf_plane_restr0.0055864
X-RAY DIFFRACTIONf_dihedral_angle_d13.92631772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.26281370.24446211X-RAY DIFFRACTION97.92
1.59-1.630.26771590.23776218X-RAY DIFFRACTION98.18
1.63-1.680.26231350.24146279X-RAY DIFFRACTION98.27
1.68-1.730.27531530.22816212X-RAY DIFFRACTION98.2
1.73-1.80.2241550.21176231X-RAY DIFFRACTION97.88
1.8-1.870.21421240.19246099X-RAY DIFFRACTION95.92
1.87-1.950.21291560.18776281X-RAY DIFFRACTION99.2
1.95-2.060.2081400.18666332X-RAY DIFFRACTION99.1
2.06-2.180.18221370.16836346X-RAY DIFFRACTION99.19
2.18-2.350.19311510.16556329X-RAY DIFFRACTION99.14
2.35-2.590.18471370.17316187X-RAY DIFFRACTION96.33
2.59-2.960.17951520.16856346X-RAY DIFFRACTION99.1
2.96-3.730.17141380.15366424X-RAY DIFFRACTION99.71
3.73-36.530.16351350.15556412X-RAY DIFFRACTION97.44

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