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- PDB-2zur: Crystal Structure of Rh(nbd)/apo-Fr -

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Basic information

Entry
Database: PDB / ID: 2zur
TitleCrystal Structure of Rh(nbd)/apo-Fr
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / Acetylation / Iron / Iron storage / Metal-binding
Function / homology
Function and homology information


ferritin complex / autolysosome / ferric iron binding / autophagosome / iron ion transport / ferrous iron binding / cytoplasmic vesicle / intracellular iron ion homeostasis / 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
: / Rhodium / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAbe, S. / Hirata, K. / Ueno, T. / Shimizu, N. / Yamamoto, M. / Takata, M. / Watanabe, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Polymerization of phenylacetylene by rhodium complexes within a discrete space of apo-ferritin
Authors: Abe, S. / Hirata, K. / Ueno, T. / Morino, K. / Shimizu, N. / Yamamoto, M. / Takata, M. / Yashima, E. / Watanabe, Y.
History
DepositionOct 28, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,52318
Polymers20,0661
Non-polymers1,45717
Water3,459192
1
X: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)516,552432
Polymers481,59524
Non-polymers34,957408
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 area114160 Å2
ΔGint-1623 kcal/mol
Surface area134200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.276, 181.276, 181.276
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
11X-175-

CD

21X-178-

CD

31X-327-

HOH

41X-362-

HOH

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 20066.465 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 , 5 types, 209 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-RH / Rhodium


Mass: 102.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rh
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5M ammonium sulfate, 10mM cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.5334 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2006
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.5334 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 24236 / % possible obs: 100 % / Redundancy: 11.6 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 38.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 9.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAT

1dat


Resolution: 1.8→37.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.684 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19618 1250 5.2 %RANDOM
Rwork0.17521 ---
obs0.1763 22956 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.801 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 49 192 1710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221537
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9982076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3895198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56523.67179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89615283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1581515
X-RAY DIFFRACTIONr_chiral_restr0.1010.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021143
X-RAY DIFFRACTIONr_nbd_refined0.2460.2792
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2160
X-RAY DIFFRACTIONr_metal_ion_refined0.1770.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.233
X-RAY DIFFRACTIONr_mcbond_it0.7731.5924
X-RAY DIFFRACTIONr_mcangle_it1.2921438
X-RAY DIFFRACTIONr_scbond_it2.1943674
X-RAY DIFFRACTIONr_scangle_it3.5624.5623
X-RAY DIFFRACTIONr_sphericity_free8.59538
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.188 86 -
Rwork0.187 1662 -
obs--100 %

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