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- PDB-4zl6: Crystal structure of the PmFTN variant E44H soaked in iron (3 h) -

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Basic information

Entry
Database: PDB / ID: 4zl6
TitleCrystal structure of the PmFTN variant E44H soaked in iron (3 h)
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 / intracellular iron ion homeostasis / identical protein binding
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: 1.9 Å
Model details3 hr 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 / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr2_symmetry / _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
B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,19130
Polymers113,8516
Non-polymers1,34024
Water12,737707
1
B: Ferritin
A: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)460,765120
Polymers455,40424
Non-polymers5,36196
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Buried area78790 Å2
ΔGint-1418 kcal/mol
Surface area136960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.720, 126.720, 170.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11E-204-

FE

21A-417-

HOH

31C-412-

HOH

41C-413-

HOH

51D-414-

HOH

61E-301-

HOH

71E-309-

HOH

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Components

#1: Protein
Ferritin /


Mass: 18975.146 Da / Num. of mol.: 6 / Mutation: E44H
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 / Iron


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 707 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
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: Mar 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→42.28 Å / Num. all: 108379 / Num. obs: 108379 / % possible obs: 99.3 % / Redundancy: 8.6 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.085 / Rsym value: 0.077 / Net I/av σ(I): 6.826 / Net I/σ(I): 16.5 / Num. measured all: 934635
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-24.80.5041.473518151740.270.5042.596.7
2-2.127.20.3332105906147140.1420.333598.7
2.12-2.279.30.2213.1131277140410.080.2218.8100
2.27-2.459.50.1445.2124308131190.0510.14412.3100
2.45-2.699.70.1056.9117330121190.0370.10516.1100
2.69-39.80.0779107820109660.0270.07721.6100
3-3.479.90.05611.19590097320.0190.05628.2100
3.47-4.259.80.05510.88145483010.0190.05534.299.9
4.25-6.019.70.0658.86289364930.0220.06536.999.8
6.01-42.2819.20.03114.73422937200.0120.03142.499.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.21data scaling
MOLREP11.1.03phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZL5

4zl5


Resolution: 1.9→42.28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.1644 / FOM work R set: 0.8655 / SU B: 2.615 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1129 / SU Rfree: 0.1132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 5415 5 %RANDOM
Rwork0.1673 ---
obs0.1691 102932 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.89 Å2 / Biso mean: 28.033 Å2 / Biso min: 6.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.9→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7511 0 24 707 8242
Biso mean--34.69 34.58 -
Num. residues----947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197853
X-RAY DIFFRACTIONr_bond_other_d0.0010.027170
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.93510725
X-RAY DIFFRACTIONr_angle_other_deg0.936316490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64425.542406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5351536
X-RAY DIFFRACTIONr_chiral_restr0.120.21191
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029244
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021856
X-RAY DIFFRACTIONr_mcbond_it2.5732.4833897
X-RAY DIFFRACTIONr_mcbond_other2.572.4823896
X-RAY DIFFRACTIONr_mcangle_it3.4773.6944901
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 377 -
Rwork0.261 7231 -
all-7608 -
obs--95.24 %

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