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- PDB-3qz3: The crystal structure of ferritin from Vibrio cholerae O1 biovar ... -

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Basic information

Entry
Database: PDB / ID: 3qz3
TitleThe crystal structure of ferritin from Vibrio cholerae O1 biovar El Tor str. N16961
ComponentsFerritin
KeywordsOXIDOREDUCTASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / all alpha ferritin-like / cytoplasmic
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 / identical protein binding / cytoplasm / 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
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsTan, K. / Mulligan, R. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of ferritin from Vibrio cholerae O1 biovar El Tor str. N16961
Authors: Tan, K. / Mulligan, R. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin
B: Ferritin
C: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1157
Polymers63,8663
Non-polymers2484
Water2,666148
1
A: Ferritin
B: Ferritin
C: Ferritin
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)512,91856
Polymers510,93124
Non-polymers1,98632
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
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area73360 Å2
ΔGint-361 kcal/mol
Surface area143940 Å2
MethodPISA
2
A: Ferritin
C: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7645
Polymers42,5782
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-8 kcal/mol
Surface area15800 Å2
MethodPISA
3
B: Ferritin
hetero molecules

B: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7024
Polymers42,5782
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
Buried area2420 Å2
ΔGint-11 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.960, 144.960, 136.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Ferritin


Mass: 21288.809 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_0078 / Plasmid: pMCSG19C / Production host: Escherichia coli (E. coli) / Strain (production host): PPK1037 / References: UniProt: Q9KVR1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M NaCl, 0.1M Bis-tris, 1.5M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→41 Å / Num. all: 42655 / Num. obs: 42655 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2095 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EUM

1eum


Resolution: 2.099→41.028 Å / SU ML: 0.23 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 2068 5.05 %random
Rwork0.1798 ---
obs0.1818 40957 95.92 %-
all-40957 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.994 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.408 Å2-0 Å20 Å2
2---7.408 Å2-0 Å2
3---14.8159 Å2
Refinement stepCycle: LAST / Resolution: 2.099→41.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 16 148 4146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074094
X-RAY DIFFRACTIONf_angle_d0.9515510
X-RAY DIFFRACTIONf_dihedral_angle_d16.631475
X-RAY DIFFRACTIONf_chiral_restr0.07585
X-RAY DIFFRACTIONf_plane_restr0.004717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0992-2.17420.31311620.2253470X-RAY DIFFRACTION87
2.1742-2.26130.25681890.19723638X-RAY DIFFRACTION91
2.2613-2.36420.22742170.18083766X-RAY DIFFRACTION94
2.3642-2.48880.23022080.19483816X-RAY DIFFRACTION95
2.4888-2.64470.26282070.21493840X-RAY DIFFRACTION96
2.6447-2.84880.2512040.20073981X-RAY DIFFRACTION98
2.8488-3.13540.25042250.20763972X-RAY DIFFRACTION99
3.1354-3.58890.24982210.18844050X-RAY DIFFRACTION100
3.5889-4.52070.18092330.15634079X-RAY DIFFRACTION100
4.5207-41.03580.18662020.16114277X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.33070.48-0.66060.7012-0.36270.28740.08750.07030.29290.0678-0.04110.057-0.0991-0.0403-0.03560.3335-0.0223-0.0160.3179-0.00210.3824-26.6685-12.7372-40.3094
20.2059-0.47610.0660.9643-0.52930.7530.09730.0387-0.0715-0.1215-0.04590.17020.14080.0626-0.0590.4476-0.0172-0.04390.3424-0.01530.3825-48.3679-8.6527-9.7293
30.6454-0.1404-0.75260.491-0.03950.823-0.0542-0.2287-0.04630.12320.0094-0.13910.04860.31050.01920.32050.0039-0.01090.376-0.00940.3297-21.4559-35.2439-27.6801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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