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- PDB-3a9q: Crystal Structure Analysis of E173A variant of the soybean ferrit... -

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Basic information

Entry
Database: PDB / ID: 3a9q
TitleCrystal Structure Analysis of E173A variant of the soybean ferritin SFER4
ComponentsFerritin-4, chloroplastic
KeywordsOXIDOREDUCTASE / 4-helix bundle / Chloroplast / Iron / Iron storage / Metal-binding / Plastid / Transit peptide
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / chloroplast / ferrous iron binding / iron ion transport / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 2. / Ferritin, conserved site / 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 iron-binding regions signature 2. / Ferritin, conserved site / 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
ACETIC ACID / Ferritin-4, chloroplastic
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsMasuda, T. / Goto, F. / Yoshihara, T. / Mikami, B.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin
Authors: Masuda, T. / Goto, F. / Yoshihara, T. / Mikami, B.
History
DepositionNov 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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_alt_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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferritin-4, chloroplastic
B: Ferritin-4, chloroplastic
C: Ferritin-4, chloroplastic
D: Ferritin-4, chloroplastic
E: Ferritin-4, chloroplastic
F: Ferritin-4, chloroplastic
G: Ferritin-4, chloroplastic
H: Ferritin-4, chloroplastic
I: Ferritin-4, chloroplastic
J: Ferritin-4, chloroplastic
K: Ferritin-4, chloroplastic
L: Ferritin-4, chloroplastic
M: Ferritin-4, chloroplastic
N: Ferritin-4, chloroplastic
O: Ferritin-4, chloroplastic
P: Ferritin-4, chloroplastic
Q: Ferritin-4, chloroplastic
R: Ferritin-4, chloroplastic
S: Ferritin-4, chloroplastic
T: Ferritin-4, chloroplastic
U: Ferritin-4, chloroplastic
V: Ferritin-4, chloroplastic
W: Ferritin-4, chloroplastic
X: Ferritin-4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)581,065166
Polymers575,01524
Non-polymers6,051142
Water61,7013425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area131420 Å2
ΔGint-590 kcal/mol
Surface area149940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.503, 221.816, 122.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ...
Ferritin-4, chloroplastic / SFerH-4


Mass: 23958.951 Da / Num. of mol.: 24 / Fragment: UNP residues 36-247 / Mutation: E173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q948P5, ferroxidase
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 124 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3425 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 15% PEG 1000, 0.2M calcium acetate, 0.1M imidazole (pH 7.8) , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 30, 2009
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.896→50 Å / Num. all: 477639 / Num. obs: 473818 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 14.64 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 8.34 / Num. unique all: 23711 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A68

3a68


Resolution: 1.896→49.674 Å / FOM work R set: 0.897 / SU ML: 0.2 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 23231 5.02 %RANDOM
Rwork0.1504 ---
obs0.1522 463041 96.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.459 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 20.595 Å2
Baniso -1Baniso -2Baniso -3
1-0.2264 Å20 Å2-0 Å2
2--3.9231 Å2-0 Å2
3----4.1495 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.896→49.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39181 0 202 3429 42812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00640270
X-RAY DIFFRACTIONf_angle_d0.8754732
X-RAY DIFFRACTIONf_dihedral_angle_d19.27515385
X-RAY DIFFRACTIONf_chiral_restr0.065918
X-RAY DIFFRACTIONf_plane_restr0.0037308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8964-1.9180.23576510.181313182X-RAY DIFFRACTION87
1.918-1.94050.22976950.165613577X-RAY DIFFRACTION91
1.9405-1.96420.21167350.163113724X-RAY DIFFRACTION91
1.9642-1.98910.22817340.176914072X-RAY DIFFRACTION94
1.9891-2.01520.23227410.167214027X-RAY DIFFRACTION93
2.0152-2.04280.20087800.156714197X-RAY DIFFRACTION95
2.0428-2.0720.20067460.156614168X-RAY DIFFRACTION94
2.072-2.10290.20667280.15614343X-RAY DIFFRACTION95
2.1029-2.13580.19757650.147814344X-RAY DIFFRACTION95
2.1358-2.17080.19647930.149414371X-RAY DIFFRACTION95
2.1708-2.20830.21387470.149914485X-RAY DIFFRACTION96
2.2083-2.24840.2088030.146914538X-RAY DIFFRACTION97
2.2484-2.29170.19937510.150714676X-RAY DIFFRACTION97
2.2917-2.33840.19467760.149914681X-RAY DIFFRACTION97
2.3384-2.38930.20137870.146514718X-RAY DIFFRACTION97
2.3893-2.44490.18637480.150114790X-RAY DIFFRACTION98
2.4449-2.5060.1968140.15314862X-RAY DIFFRACTION98
2.506-2.57370.19437870.153714823X-RAY DIFFRACTION98
2.5737-2.64950.18747330.150614924X-RAY DIFFRACTION98
2.6495-2.7350.18768100.156914945X-RAY DIFFRACTION99
2.735-2.83270.18487530.15414982X-RAY DIFFRACTION99
2.8327-2.94610.1847660.148815051X-RAY DIFFRACTION99
2.9461-3.08020.16978120.143915076X-RAY DIFFRACTION99
3.0802-3.24260.17917820.151515148X-RAY DIFFRACTION100
3.2426-3.44570.16458170.142415160X-RAY DIFFRACTION100
3.4457-3.71160.16878260.136215197X-RAY DIFFRACTION100
3.7116-4.0850.15518510.124215211X-RAY DIFFRACTION100
4.085-4.67570.13798160.116315306X-RAY DIFFRACTION100
4.6757-5.88940.16158000.140915470X-RAY DIFFRACTION100
5.8894-49.69140.17558840.176215762X-RAY DIFFRACTION100

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