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- PDB-4zkh: Crystal structure of the PmFTN variant E44Q soaked in iron (overnight) -

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Basic information

Entry
Database: PDB / ID: 4zkh
TitleCrystal structure of the PmFTN variant E44Q soaked in iron (overnight)
ComponentsFerritin
KeywordsOXIDOREDUCTASE / ferritin / di-iron ferroxidase centre / 4-helix bundle
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / identical protein binding / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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 speciesPseudo-nitzschia multiseries (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
Model detailsovernight soaked
AuthorsPfaffen, S. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Diatom Ferritin Optimized for Iron Oxidation but Not Iron Storage.
Authors: Pfaffen, S. / Bradley, J.M. / Abdulqadir, R. / Firme, M.R. / Moore, G.R. / Le Brun, N.E. / Murphy, M.E.
History
DepositionApr 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_keywords.pdbx_keywords

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)153,45239
Polymers151,7218
Non-polymers1,73131
Water15,763875
1
A: Ferritin
D: Ferritin
B: Ferritin
C: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)460,357117
Polymers455,16324
Non-polymers5,19493
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)175.250, 175.250, 175.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-410-

HOH

31D-407-

HOH

41B-397-

HOH

51B-412-

HOH

61B-413-

HOH

71G-398-

HOH

81H-391-

HOH

91H-399-

HOH

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Components

#1: Protein
Ferritin


Mass: 18965.129 Da / Num. of mol.: 8 / Mutation: E44Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudo-nitzschia multiseries (Diatom) / Gene: FTN / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B6DMH6, ferroxidase
#2: Chemical...
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodiaum acetate pH 5.5, Ammonium sulfate, NaCl / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.61 Å / Num. all: 140366 / Num. obs: 140366 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.032 / Rrim(I) all: 0.12 / Rsym value: 0.11 / Net I/σ(I): 15.9 / Num. measured all: 1882556
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym value% possible all
1.9-212.10.9772.5245703203850.0110.035100
6.01-48.6114.60.03541.36798546650.0140.04899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREP11.1.03phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IWJ

4iwj


Resolution: 1.9→48.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.1882 / WRfactor Rwork: 0.1544 / FOM work R set: 0.8737 / SU B: 2.7 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1115 / SU Rfree: 0.1113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 7045 5 %RANDOM
Rwork0.1623 ---
obs0.1641 133305 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.66 Å2 / Biso mean: 27.793 Å2 / Biso min: 11.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10040 0 31 875 10946
Biso mean--30.04 33.63 -
Num. residues----1266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910533
X-RAY DIFFRACTIONr_bond_other_d0.0010.029599
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.93714381
X-RAY DIFFRACTIONr_angle_other_deg0.916322065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09551324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.72225.673550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.074151714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4671549
X-RAY DIFFRACTIONr_chiral_restr0.110.21589
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212451
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022494
X-RAY DIFFRACTIONr_mcbond_it2.4662.4935221
X-RAY DIFFRACTIONr_mcbond_other2.4652.4925220
X-RAY DIFFRACTIONr_mcangle_it3.3143.7126570
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 508 -
Rwork0.266 9848 -
all-10356 -
obs--100 %

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