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- PDB-3e19: Crystal Structure of Iron Uptake Regulatory Protein (FeoA) Solved... -

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Basic information

Entry
Database: PDB / ID: 3.0E+19
TitleCrystal Structure of Iron Uptake Regulatory Protein (FeoA) Solved by Sulfur SAD in a Monoclinic Space Group
ComponentsFeoA
KeywordsTRANSCRIPTION REGULATOR / METAL BINDING PROTEIN / transcriptional regulator / metal-binding / iron uptake / beta-barrel
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
PHOSPHATE ION / FeoA
Similarity search - Component
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHughes, R.C. / Li, Y. / Wang, B.-C. / Liu, Z.-J. / Ng, J.D.
CitationJournal: To be Published
Title: Crystallographic Structure Determination of Iron Uptake Regulatory Protein (FeoA) by Sulfur SAD in a Monoclinic Space Group
Authors: Hughes, R.C. / Li, Y. / Wang, B.-C. / Liu, Z.-J. / Ng, J.D.
History
DepositionAug 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 40MOLPROBITY STRUCTURE VALIDATION AUTHORS : I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK, : G.J.KAPRAL,X. ...MOLPROBITY STRUCTURE VALIDATION AUTHORS : I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK, : G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL, : J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON REFERENCE : MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE : VALIDATION FOR PROTEINS AND NUCLEIC ACIDS : NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,1186
Polymers31,9314
Non-polymers1872
Water3,261181
1
A: FeoA
B: FeoA
C: FeoA
D: FeoA
hetero molecules

A: FeoA
B: FeoA
C: FeoA
D: FeoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,23612
Polymers63,8618
Non-polymers3744
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area11430 Å2
ΔGint-106 kcal/mol
Surface area23930 Å2
MethodPISA
2
A: FeoA
B: FeoA
C: FeoA
D: FeoA
hetero molecules

A: FeoA
B: FeoA
C: FeoA
D: FeoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,23612
Polymers63,8618
Non-polymers3744
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11450 Å2
ΔGint-102 kcal/mol
Surface area23910 Å2
MethodPISA
3
A: FeoA
D: FeoA
hetero molecules

A: FeoA
D: FeoA
hetero molecules

B: FeoA
C: FeoA
hetero molecules

B: FeoA
C: FeoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,23612
Polymers63,8618
Non-polymers3744
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_554-x,y,-z-11
Buried area9880 Å2
ΔGint-96 kcal/mol
Surface area25470 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.786, 68.386, 68.969
Angle α, β, γ (deg.)90.00, 132.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
FeoA


Mass: 7982.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Strain: OGL-20 / Gene: OGL-20_FeoA / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWU5*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium Phosphate, Potassium Phosphate, pH 7.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11.9
SYNCHROTRONAPS 22-ID21.9
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDDec 9, 2007
MARMOSAIC 300 mm CCD2CCDDec 9, 2007
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionRedundancy: 22.5 % / Av σ(I) over netI: 33.8 / Number: 454770 / Rmerge(I) obs: 0.048 / Χ2: 1.44 / D res high: 2 Å / D res low: 50 Å / Num. obs: 20216 / % possible obs: 92.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315098.210.041.37922.5
3.424.3196.410.0411.43623.1
2.993.4295.310.0471.5823.2
2.712.9994.210.0531.55623.2
2.522.7193.210.0571.44123.1
2.372.529210.0621.36423.1
2.252.379110.0661.31622.9
2.152.259010.0741.37922.3
2.072.1589.310.0851.38121.7
22.0786.710.1041.56919.5
ReflectionResolution: 2→50 Å / Num. obs: 20216 / % possible obs: 92.7 % / Redundancy: 22.5 % / Rmerge(I) obs: 0.048
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.0719.50.1041,286.7
2.07-2.1521.70.0851,289.3
2.15-2.2522.30.0741,290
2.25-2.3722.90.0661,291
2.37-2.5223.10.0621,292
2.52-2.7123.10.0571,293.2
2.71-2.9923.20.0531,294.2
2.99-3.4223.20.0471,295.3
3.42-4.3123.10.0411,296.4
4.31-5022.50.041,298.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: ab initio

Resolution: 2→19.34 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 3.351 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22789 1039 5.2 %RANDOM
Rwork0.17291 ---
obs0.17576 19064 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 11 181 2326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222186
X-RAY DIFFRACTIONr_bond_other_d0.0040.021536
X-RAY DIFFRACTIONr_angle_refined_deg1.8642.022938
X-RAY DIFFRACTIONr_angle_other_deg1.15433788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.3355297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09821.88753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2011517
X-RAY DIFFRACTIONr_chiral_restr0.240.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.2210.2362
X-RAY DIFFRACTIONr_nbd_other0.1990.21612
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21043
X-RAY DIFFRACTIONr_nbtor_other0.0890.21229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1490.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3731.51527
X-RAY DIFFRACTIONr_mcbond_other0.2871.5627
X-RAY DIFFRACTIONr_mcangle_it2.03222353
X-RAY DIFFRACTIONr_scbond_it3.1983735
X-RAY DIFFRACTIONr_scangle_it5.1454.5583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 83 -
Rwork0.17 1265 -
obs--100 %

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