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- PDB-1xvy: Crystal Structure of iron-free Serratia marcescens SfuA -

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Basic information

Entry
Database: PDB / ID: 1xvy
TitleCrystal Structure of iron-free Serratia marcescens SfuA
ComponentssfuA
Keywordsiron binding protein / periplasmic iron binding protein
Function / homology
Function and homology information


iron ion transport / transmembrane transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Ferric binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / 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
CITRIC ACID / Fe(3+)-binding periplasmic protein
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsShouldice, S.R. / McRee, D.E. / Dougan, D.R. / Tari, L.W. / Schryvers, A.B.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Novel Anion-independent Iron Coordination by Members of a Third Class of Bacterial Periplasmic Ferric Ion-binding Proteins
Authors: Shouldice, S.R. / McRee, D.E. / Dougan, D.R. / Tari, L.W. / Schryvers, A.B.
History
DepositionOct 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: sfuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5102
Polymers33,3181
Non-polymers1921
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.046, 65.392, 50.266
Angle α, β, γ (deg.)90.00, 111.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein sfuA


Mass: 33317.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: sfuA / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: P21408
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 4
Details: lithium chloride, PEG 6000, citric acid, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 15, 2004
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→24.88 Å / Num. obs: 27910 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.74→1.8 Å / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1xvx

1xvx


Resolution: 1.74→46.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.344 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20927 1414 5.1 %RANDOM
Rwork0.16248 ---
all0.165 27026 --
obs0.16495 26494 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.729 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0.47 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.74→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 13 424 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222397
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9573255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7525.55699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28915394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.901156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021813
X-RAY DIFFRACTIONr_nbd_refined0.2030.21330
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21684
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.231
X-RAY DIFFRACTIONr_mcbond_it0.7211.51556
X-RAY DIFFRACTIONr_mcangle_it1.13522430
X-RAY DIFFRACTIONr_scbond_it2.243965
X-RAY DIFFRACTIONr_scangle_it3.4374.5825
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 85 -
Rwork0.295 1917 -
obs--95.56 %

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