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- PDB-4zlw: Crystal structure of the PmFTN variant E130A soaked in iron (over... -

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Basic information

Entry
Database: PDB / ID: 4zlw
TitleCrystal structure of the PmFTN variant E130A 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 / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / identical protein binding / cytoplasm
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 speciesPseudo-nitzschia multiseries (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionMay 1, 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
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
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_seq_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

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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)152,53845
Polymers150,4728
Non-polymers2,06637
Water9,188510
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)457,613135
Polymers451,41524
Non-polymers6,199111
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)175.051, 175.051, 175.051
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
11D-361-

HOH

21B-357-

HOH

31B-359-

HOH

41G-364-

HOH

51H-364-

HOH

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Components

#1: Protein
Ferritin


Mass: 18808.945 Da / Num. of mol.: 8 / Fragment: iron storage protein / Mutation: E130A
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.: 37 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
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: Jan 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.55 Å / Num. all: 120022 / Num. obs: 120022 / % possible obs: 100 % / Redundancy: 13.9 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.115 / Rsym value: 0.107 / Net I/av σ(I): 5.63 / Net I/σ(I): 14.9 / Num. measured all: 1670804
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.1113.71.1350.7237246173800.331.1352.4100
2.11-2.2413.80.7171.1228273165520.2070.7173.7100
2.24-2.3913.90.4821.6215981154890.1380.4825.5100
2.39-2.5814.10.3222.4203674144500.0920.3228.2100
2.58-2.8314.10.2053.8188021132940.0580.20512.1100
2.83-3.1614.20.1196.3172064121020.0340.11918.8100
3.16-3.6514.10.0788.8150836106680.0220.07828.7100
3.65-4.4713.40.0738.112188890650.0210.07336.8100
4.47-6.3213.60.04811.79661670800.0140.04839100
6.32-46.78414.30.02522.25620539420.0080.0254598.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREP11.0.05phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZKH

4zkh


Resolution: 2→48.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2181 / WRfactor Rwork: 0.1787 / FOM work R set: 0.8407 / SU B: 3.978 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1457 / SU Rfree: 0.1409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 6015 5 %RANDOM
Rwork0.1866 ---
obs0.1886 113996 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.9 Å2 / Biso mean: 40.874 Å2 / Biso min: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9927 0 37 510 10474
Biso mean--58.59 42.49 -
Num. residues----1258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910243
X-RAY DIFFRACTIONr_bond_other_d0.0010.029393
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.93813968
X-RAY DIFFRACTIONr_angle_other_deg0.887321587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26151278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95625.585530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.836151652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2411548
X-RAY DIFFRACTIONr_chiral_restr0.1080.21561
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022402
X-RAY DIFFRACTIONr_mcbond_it3.4113.7435094
X-RAY DIFFRACTIONr_mcbond_other3.4093.7435093
X-RAY DIFFRACTIONr_mcangle_it4.5115.5866378
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 446 -
Rwork0.283 8383 -
all-8829 -
obs--100 %

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