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- PDB-3wvw: Crystal structure of RuCO/apo-WTFr -

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Basic information

Entry
Database: PDB / ID: 3wvw
TitleCrystal structure of RuCO/apo-WTFr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / IRON STORAGE
Function / homology
Function and homology information


intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / 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
: / RUTHENIUM ION / bis(oxidaniumylidynemethyl)ruthenium(2+) / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFujita, K. / Tanaka, Y. / Abe, S. / Hikage, T. / Kuchimaru, T. / Kizaka-Kondoh, S. / Ueno, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Intracellular CO release from composite of ferritin and ruthenium carbonyl complexes.
Authors: Fujita, K. / Tanaka, Y. / Sho, T. / Ozeki, S. / Abe, S. / Hikage, T. / Kuchimaru, T. / Kizaka-Kondoh, S. / Ueno, T.
History
DepositionJun 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,16116
Polymers19,8721
Non-polymers1,28915
Water2,450136
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)507,876384
Polymers476,93824
Non-polymers30,938360
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 area99970 Å2
ΔGint-510 kcal/mol
Surface area138550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.863, 181.863, 181.863
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-201-

CD

21A-202-

CD

31A-203-

CD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ferritin light chain / / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Plasmid: pMK2 / Production host: Escherichia coli (E. coli) / Strain (production host): Nova Blue / References: UniProt: P02791

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Non-polymers , 6 types, 151 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-RU / RUTHENIUM ION / Ruthenium


Mass: 101.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ru
#6: Chemical ChemComp-RU1 / bis(oxidaniumylidynemethyl)ruthenium(2+)


Mass: 157.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O2Ru
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1M ammonium sulfate, 20 mM cadmium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 17, 2014
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17978 / % possible obs: 99.9 % / Redundancy: 20.5 % / Biso Wilson estimate: 16.16 Å2 / Net I/σ(I): 44.51
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAT

1dat


Resolution: 2→21.43 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.504 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19917 919 5.1 %RANDOM
Rwork0.15794 ---
obs0.16004 17054 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→21.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 47 136 1572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191470
X-RAY DIFFRACTIONr_bond_other_d0.0010.021427
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9871963
X-RAY DIFFRACTIONr_angle_other_deg0.99133269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5165178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65324.15677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47415267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8471512
X-RAY DIFFRACTIONr_chiral_restr0.130.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02352
X-RAY DIFFRACTIONr_mcbond_it2.0851.727700
X-RAY DIFFRACTIONr_mcbond_other2.0371.72699
X-RAY DIFFRACTIONr_mcangle_it3.232.565876
X-RAY DIFFRACTIONr_mcangle_other3.2292.574877
X-RAY DIFFRACTIONr_scbond_it3.4052.176769
X-RAY DIFFRACTIONr_scbond_other3.372.167765
X-RAY DIFFRACTIONr_scangle_other5.1283.0611082
X-RAY DIFFRACTIONr_long_range_B_refined7.09614.8111763
X-RAY DIFFRACTIONr_long_range_B_other7.02614.5441719
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 69 -
Rwork0.149 1228 -
obs--100 %

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