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- PDB-1krq: CRYSTAL STRUCTURE ANALYSIS OF CAMPYLOBACTER JEJUNI FERRITIN -

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Basic information

Entry
Database: PDB / ID: 1krq
TitleCRYSTAL STRUCTURE ANALYSIS OF CAMPYLOBACTER JEJUNI FERRITIN
Componentsferritin
KeywordsMETAL BINDING PROTEIN / bacterial non-heme ferritin / H-chain like four-helix bundle
Function / homology
Function and homology information


bacterial non-heme ferritin / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / 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 speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHortolan, L. / Saintout, N. / Granier, G. / Langlois d'Estaintot, B. / Manigand, C. / Mizunoe, Y. / Wai, S.N. / Gallois, B. / Precigoux, G.
CitationJournal: To be Published
Title: STRUCTURE OF CAMPYLOBACTER JEJUNI FERRITIN AT 2.7 A RESOLUTION
Authors: Hortolan, L. / Saintout, N. / Granier, G. / Langlois d'Estaintot, B. / Manigand, C. / Mizunoe, Y. / Wai, S.N. / Gallois, B. / Precigoux, G.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 525SOLVENT WATER MOLECULES HOH 200 AND HOH 201 BIND THE PROTEIN AT THE FERROXYDASE CENTER (INVOLVED ...SOLVENT WATER MOLECULES HOH 200 AND HOH 201 BIND THE PROTEIN AT THE FERROXYDASE CENTER (INVOLVED RESIDUES: GLU 17, GLU 50, HIS 53, GLU 94, GLU 126, GLU 129 and GLU 130) PREVIOUSLY DESCRIBED IN THE FERRITIN OF E.Coli (PDB entry code 1EUM) AND THUS COULD STAND FOR IRON IONS WITH LOW OCCUPANCY FACTORS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ferritin


Theoretical massNumber of molelcules
Total (without water)19,5111
Polymers19,5111
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: ferritin
x 24


Theoretical massNumber of molelcules
Total (without water)468,26424
Polymers468,26424
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
MethodPQS
Unit cell
Length a, b, c (Å)152.050, 152.050, 152.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein ferritin


Mass: 19510.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cft / Plasmid: pET3b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q46106
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.95 Å3/Da / Density % sol: 68.62 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, PEG400, Hepes, Sodium azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.966 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 2000 / Details: W/Si mutilayer mirror
RadiationMonochromator: focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.7→19 Å / Num. all: 8373 / Num. obs: 8373 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 44.75 Å2 / Rsym value: 0.064 / Net I/σ(I): 5.9
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.38 / % possible all: 99.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FHA

2fha


Resolution: 2.7→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 399 5 %RANDOM
Rwork0.203 ---
all0.205 8368 --
obs0.205 8368 98.5 %-
Solvent computationSolvent model: CALCULATED FROM COORDINATES / Bsol: 64.48 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-15 Å
Luzzati sigma a0.48 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 0 4 1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.05
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.454
X-RAY DIFFRACTIONc_mcangle_it4.574
X-RAY DIFFRACTIONc_scbond_it5.654
X-RAY DIFFRACTIONc_scangle_it7.656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
2.7-2.820.389520.285X-RAY DIFFRACTION
2.82-2.970.3530.265X-RAY DIFFRACTION
2.97-3.150.338430.239X-RAY DIFFRACTION
3.15-3.40.246500.186X-RAY DIFFRACTION
3.4-3.730.234580.194X-RAY DIFFRACTION
3.73-4.260.234430.192X-RAY DIFFRACTION

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