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- PDB-3egm: Structural basis of iron transport gating in Helicobacter pylori ... -

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Basic information

Entry
Database: PDB / ID: 3egm
TitleStructural basis of iron transport gating in Helicobacter pylori ferritin
ComponentsFerritin
KeywordsOXIDOREDUCTASE / iron storage / Iron / Metal-binding
Function / homology
Function and homology information


bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / identical protein binding / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Bacterial non-heme ferritin
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsKim, K.H. / Cho, K.J. / Shin, H.J. / Lee, J.H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The crystal structure of ferritin from Helicobacter pylori reveals unusual conformational changes for iron uptake.
Authors: Cho, K.J. / Shin, H.J. / Lee, J.H. / Kim, K.J. / Park, S.S. / Lee, Y. / Lee, C. / Park, S.S. / Kim, K.H.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,61324
Polymers125,4996
Non-polymers1,11418
Water15,997888
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)506,45096
Polymers501,99424
Non-polymers4,45672
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area101310 Å2
ΔGint-1233 kcal/mol
Surface area137120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.528, 128.528, 165.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11E-170-

FE

21F-170-

FE

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Components

#1: Protein
Ferritin


Mass: 20916.434 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: ftnA, pfr, jhp_0598 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZLI1, ferroxidase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 888 / 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: 2.72 Å3/Da / Density % sol: 54.8 % / Mosaicity: 0.396 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 10% isopropanol, 200mM Sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 78025 / Num. obs: 78025 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.131 / Χ2: 0.993 / Net I/σ(I): 22.333
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.409 / Num. unique all: 7763 / Χ2: 0.968 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.1→29.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.12 / SU B: 7.966 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3921 5 %RANDOM
Rwork0.162 ---
obs0.164 77982 100 %-
all-77982 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100.83 Å2 / Biso mean: 14.991 Å2 / Biso min: 3.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8436 0 33 888 9357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0218892
X-RAY DIFFRACTIONr_angle_refined_deg0.9481.92512036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5351081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67726.029481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.049151615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.199156
X-RAY DIFFRACTIONr_chiral_restr0.0790.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026832
X-RAY DIFFRACTIONr_nbd_refined0.1890.24421
X-RAY DIFFRACTIONr_nbtor_refined0.2930.26266
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2772
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.2177
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.280
X-RAY DIFFRACTIONr_mcbond_it0.6391.55487
X-RAY DIFFRACTIONr_mcangle_it1.00828530
X-RAY DIFFRACTIONr_scbond_it1.53933906
X-RAY DIFFRACTIONr_scangle_it2.3994.53497
X-RAY DIFFRACTIONr_rigid_bond_restr0.95239393
X-RAY DIFFRACTIONr_sphericity_free2.7223903
X-RAY DIFFRACTIONr_sphericity_bonded1.22338664
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 300 -
Rwork0.158 5479 -
all-5779 -
obs--100 %

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