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- PDB-2pt2: Structure of FutA1 with Iron(II) -

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Basic information

Entry
Database: PDB / ID: 2pt2
TitleStructure of FutA1 with Iron(II)
ComponentsIron transport protein
KeywordsMETAL TRANSPORT / C-clamp / iron-binding protein / solute-binding protein / periplasmic binding protein / ABC transporter
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / iron ion transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Ferric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Iron uptake protein A1
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoropatkin, N.M. / Randich, A.M. / Bhattachryya-Pakrasi, M. / Pakrasi, H.B. / Smith, T.J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The structure of the iron-binding protein, FutA1, from Synechocystis 6803.
Authors: Koropatkin, N. / Randich, A.M. / Bhattacharyya-Pakrasi, M. / Pakrasi, H.B. / Smith, T.J.
History
DepositionMay 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1097
Polymers36,6071
Non-polymers5026
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.307, 65.703, 50.255
Angle α, β, γ (deg.)90.000, 102.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Iron transport protein


Mass: 36606.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Description: modified to contain an rTEV cleavage site / Gene: FUTA1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P72827
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 298 K / Method: batch seeding / pH: 8
Details: 100mM HEPPS, 2.2-2.8 ammonium sulfate, , pH 8.0, batch seeding, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97167 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 16, 2006 / Details: mirrors
RadiationMonochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97167 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 20599 / Num. obs: 20599 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.113 / Net I/σ(I): 43.7
Reflection shellResolution: 2→2.02 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 20.8 / Num. unique all: 505 / Rsym value: 0.145 / % possible all: 86.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FutA1; entry 2PT1

2pt1


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2035 9.6 %random
Rwork0.175 ---
all0.175 20599 --
obs0.175 20599 97 %-
Solvent computationBsol: 40.887 Å2
Displacement parametersBiso mean: 19.348 Å2
Baniso -1Baniso -2Baniso -3
1--2.954 Å20 Å2-5.251 Å2
2---1.342 Å20 Å2
3---4.296 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 25 318 2798
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.204
X-RAY DIFFRACTIONc_mcbond_it1.1741.5
X-RAY DIFFRACTIONc_scbond_it2.0992
X-RAY DIFFRACTIONc_mcangle_it1.7152
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2→2.02 Å
RfactorNum. reflection% reflection
Rfree0.2287 64 -
Rwork0.1858 --
obs-505 86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5eg.parameg.top

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