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- PDB-3rav: Horse spleen apo-ferritin with bound Pentobarbital -

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Basic information

Entry
Database: PDB / ID: 3rav
TitleHorse spleen apo-ferritin with bound Pentobarbital
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / 4-HELIX BUNDLE / 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 / Ferritin, core subunit, four-helix bundle / 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 / Ferritin, core subunit, four-helix bundle / 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
: / Chem-RAV / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / molecular replacement / Resolution: 1.9 Å
AuthorsOakley, S.H. / Vedula, L.S. / Xi, J. / Liu, R. / Eckenhoff, R.G. / Loll, P.J.
CitationJournal: to be published
Title: High resolution view of barbiturate recognition by a protein binding site
Authors: Oakley, S.H. / Vedula, L.S. / Xi, J. / Liu, R. / Eckenhoff, R.G. / Loll, P.J.
History
DepositionMar 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 11, 2019Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] ..._pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
A: Ferritin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,96510
Polymers19,8721
Non-polymers1,0939
Water3,531196
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)503,167240
Polymers476,93824
Non-polymers26,229216
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 area99270 Å2
ΔGint-879 kcal/mol
Surface area134620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.480, 182.480, 182.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-175-

CD

21A-183-

RAV

31A-183-

RAV

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Components

#1: Protein Ferritin light chain / Ferritin L subunit


Mass: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: Spleen / References: UniProt: P02791
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / 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-RAV / 5-ethyl-5-[(2S)-pentan-2-yl]pyrimidine-2,4,6(1H,3H,5H)-trione / Pentobarbital


Mass: 226.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.3 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2-1.6 M (NH4)2SO4 and 0.1-0.275 M CdSO4, 0.5 mM thiopental were mixed with equal volumes of apoferritin solution and equilibrated over 0.7-1 mL, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9774 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.9→45.62 Å / Num. all: 21095 / Num. obs: 21095 / % possible obs: 100 % / Observed criterion σ(F): 38.9 / Observed criterion σ(I): 7.8 / Redundancy: 34.09 % / Biso Wilson estimate: 21.63 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 34.09 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 7.8 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.24 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.62 Å
Translation2.5 Å45.62 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Resolution: 1.9→45.62 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.2 / σ(F): 0.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1994 5.15 %RANDOM
Rwork0.174 ---
all0.176 21101 --
obs0.176 21072 99.9 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.874 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 75.75 Å2 / Biso mean: 22.472 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 32 196 1574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071461
X-RAY DIFFRACTIONf_angle_d0.9591981
X-RAY DIFFRACTIONf_chiral_restr0.065218
X-RAY DIFFRACTIONf_plane_restr0.003253
X-RAY DIFFRACTIONf_dihedral_angle_d15.726555
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9470.2621160.2332605272199
1.947-20.2451690.20626022771100
2-2.0590.2261580.18626082766100
2.059-2.1250.1821270.17626572784100
2.125-2.2010.2271540.16225882742100
2.201-2.290.2011680.16625972765100
2.29-2.3940.2071530.1726082761100
2.394-2.520.2481250.16626152740100
2.52-2.6780.1741570.16226332790100
2.678-2.8850.2011440.15926252769100
2.885-3.1750.2361470.16126012748100
3.175-3.6340.2091200.15926542774100
3.634-4.5780.1791090.16126692778100
4.578-45.6330.21470.20926402787100

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