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- PDB-5xhi: Crystal structure of Frog M-ferritin D38A mutant -

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Basic information

Entry
Database: PDB / ID: 5xhi
TitleCrystal structure of Frog M-ferritin D38A mutant
ComponentsFerritin, middle subunit
KeywordsOXIDOREDUCTASE / Ferritin / M-ferritin
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin iron-binding regions signature 1. / 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 iron-binding regions signature 1. / 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
Ferritin, middle subunit
Similarity search - Component
Biological speciesRana catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsJagdev, M.K. / Vasudevan, D.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Surface charge dependent separation of modified and hybrid ferritin in native PAGE: Impact of lysine 104
Authors: Subhadarshanee, B. / Mohanty, A. / Jagdev, M.K. / Vasudevan, D. / Behera, R.K.
History
DepositionApr 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin, middle subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,58539
Polymers20,3611
Non-polymers1,22538
Water4,828268
1
A: Ferritin, middle subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)518,052936
Polymers488,66224
Non-polymers29,390912
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area91670 Å2
ΔGint-337 kcal/mol
Surface area137510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.090, 184.090, 184.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-204-

MG

21A-206-

MG

31A-207-

MG

41A-208-

MG

51A-210-

MG

61A-211-

MG

71A-320-

HOH

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Components

#1: Protein Ferritin, middle subunit / Ferritin M / Ferritin H' / Ferritin X


Mass: 20360.896 Da / Num. of mol.: 1 / Mutation: D38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Production host: Escherichia coli BL21(DE3)pLysS (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P07798, ferroxidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3.16 Å3/Da / Density % sol: 61.05 % / Description: Cubic
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 2.0 M MgCl2 and 100 mM Bicine (pH 9.0)

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8266 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.26→31.12 Å / Num. obs: 72072 / % possible obs: 100 % / Redundancy: 14.5 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLM7.1.1data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KA3

3ka3


Resolution: 1.26→31.12 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.862 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15287 3653 5.1 %RANDOM
Rwork0.12538 ---
obs0.12676 68326 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.99 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.26→31.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 38 268 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191594
X-RAY DIFFRACTIONr_bond_other_d0.0010.021472
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.952170
X-RAY DIFFRACTIONr_angle_other_deg0.83533460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8715213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43824.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29315320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9141511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021815
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02332
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2020.823739
X-RAY DIFFRACTIONr_mcbond_other1.110.817738
X-RAY DIFFRACTIONr_mcangle_it1.3711.235933
X-RAY DIFFRACTIONr_mcangle_other1.3811.241934
X-RAY DIFFRACTIONr_scbond_it3.5841.168855
X-RAY DIFFRACTIONr_scbond_other3.5811.168855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2031.6371216
X-RAY DIFFRACTIONr_long_range_B_refined3.91312.3452041
X-RAY DIFFRACTIONr_long_range_B_other3.46211.2321953
X-RAY DIFFRACTIONr_rigid_bond_restr7.05133066
X-RAY DIFFRACTIONr_sphericity_free24.7245186
X-RAY DIFFRACTIONr_sphericity_bonded8.9653138
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.152 267 -
Rwork0.137 4960 -
obs--100 %

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