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- PDB-3ufh: Crystal structure of UndA with Iron Citrate bound -

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Basic information

Entry
Database: PDB / ID: 3ufh
TitleCrystal structure of UndA with Iron Citrate bound
ComponentsUndA
KeywordsTRANSPORT PROTEIN / C-type cytochrome / Electron transfer / c-type hemes / outermembrane
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
Decahaem cytochrome, c-type, OmcA/MtrC / Cytochrome c-552/4 / Cytochrome c554 and c-prime / Multiheme cytochrome superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / CITRATE ANION / HEME C / OXYGEN ATOM / UndA
Similarity search - Component
Biological speciesShewanella sp. HRCR_06 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsEdwards, M.J. / Clarke, T.A.
CitationJournal: Structure / Year: 2012
Title: The Crystal Structure of the Extracellular 11-heme Cytochrome UndA Reveals a Conserved 10-heme Motif and Defined Binding Site for Soluble Iron Chelates.
Authors: Edwards, M.J. / Hall, A. / Shi, L. / Fredrickson, J.K. / Zachara, J.M. / Butt, J.N. / Richardson, D.J. / Clarke, T.A.
History
DepositionNov 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UndA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,22023
Polymers92,4851
Non-polymers7,73522
Water14,916828
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.880, 106.530, 151.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UndA


Mass: 92485.195 Da / Num. of mol.: 1 / Fragment: Soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. HRCR_06 (bacteria) / Gene: undA / Plasmid: pBAD / Production host: Shewanella oneidensis (bacteria) / Strain (production host): MR-1 / References: UniProt: F8UWD6

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Non-polymers , 8 types, 850 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#7: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / 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: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, 50 mM NaCl, 50 mM MgCl2, 15% PEG5000, 20% Glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.17→63.48 Å / Num. obs: 59175 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Rsym value: 0.094 / Net I/σ(I): 5.9
Reflection shellResolution: 2.17→2.29 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.411 / % possible all: 97

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→61.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.488 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21078 2800 5.1 %RANDOM
Rwork0.16296 ---
obs0.16545 52335 100 %-
all-55989 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2--1.23 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.23→61.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5948 0 525 828 7301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226678
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5412.1699244
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9045801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32825250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04515943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4151519
X-RAY DIFFRACTIONr_chiral_restr0.1160.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0215167
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5491.53982
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.59326409
X-RAY DIFFRACTIONr_scbond_it4.28132696
X-RAY DIFFRACTIONr_scangle_it5.9284.52835
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 193 -
Rwork0.222 3781 -
obs--100 %

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