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- PDB-1xz3: Complex of apoferritin with isoflurane -

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Basic information

Entry
Database: PDB / ID: 1xz3
TitleComplex of apoferritin with isoflurane
ComponentsFerritin light chain
KeywordsMETAL BINDING PROTEIN / 4-helix bundle
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
: / Chem-ICF / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsLiu, R. / Loll, P.J. / Eckenhoff, R.G.
CitationJournal: Faseb J. / Year: 2005
Title: Structural basis for high-affinity volatile anesthetic binding in a natural 4-helix bundle protein.
Authors: Liu, R. / Loll, P.J. / Eckenhoff, R.G.
History
DepositionNov 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / 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_database_remark.text / _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.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Author states that residue 93 is indeed a LEU.

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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)20,8449
Polymers19,8721
Non-polymers9718
Water3,423190
1
A: Ferritin light chain
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)500,251216
Polymers476,93824
Non-polymers23,313192
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 area98530 Å2
ΔGint-461 kcal/mol
Surface area132280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)181.510, 181.510, 181.510
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-1001-

CD

21A-1002-

CD

DetailsBiological unit is 24-mer: x,y,z; -x,-y,z; -x,y,-z; x,-y,-z; z,x,y; z,-x,-y; -z,-x,y; -z,x,-y; y,z,x; -y,z,-x; y,-z,-x; -y,-z,x; y,x,-z; -y,-x,-z; y,-x,z; -y,x,z; x,z,-y; -x,z,y; -x,-z,-y; x,-z,y; z,y,-x; z,-y,x; -z,y,x; -z,-y,-x;

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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.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ICF / 1-CHLORO-2,2,2-TRIFLUOROETHYL DIFLUOROMETHYL ETHER / ISOFLURANE / Isoflurane


Mass: 184.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2ClF5O / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 60.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: cadmium sulfate, HEPES, sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0722 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2004
Details: parabolic collimating mirror upstream of monochromator
RadiationMonochromator: parabolic collimating mirror upstream of monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 1.74→30 Å / Num. all: 25454 / Num. obs: 25454 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.6
Reflection shellResolution: 1.74→1.82 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2551 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GWG

1gwg


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.185 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21046 1287 5.1 %RANDOM
Rwork0.17889 ---
all0.1804 23916 --
obs0.1804 23916 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.404 Å2
Refine analyzeLuzzati coordinate error obs: 0.097 Å / Luzzati d res low obs: 0.098 Å
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 17 190 1561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211405
X-RAY DIFFRACTIONr_bond_other_d0.0020.021276
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9761893
X-RAY DIFFRACTIONr_angle_other_deg0.79732958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4975170
X-RAY DIFFRACTIONr_chiral_restr0.0740.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021566
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02298
X-RAY DIFFRACTIONr_nbd_refined0.2770.2358
X-RAY DIFFRACTIONr_nbd_other0.250.21431
X-RAY DIFFRACTIONr_nbtor_other0.0850.2787
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2160
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.223
X-RAY DIFFRACTIONr_mcbond_it0.7971.5839
X-RAY DIFFRACTIONr_mcangle_it1.61821334
X-RAY DIFFRACTIONr_scbond_it2.7583566
X-RAY DIFFRACTIONr_scangle_it4.794.5558
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 87 -
Rwork0.336 1361 -
obs-1448 78.1 %
Refinement TLS params.Method: refined / Origin x: 28.5037 Å / Origin y: 9.6383 Å / Origin z: 39.6426 Å
111213212223313233
T0.0144 Å2-0.0068 Å2-0.0113 Å2-0.0038 Å20.0019 Å2--0.0289 Å2
L0.4196 °20.1091 °2-0.2234 °2-0.1391 °2-0.0439 °2--0.2657 °2
S0.0139 Å °-0.0166 Å °0.0331 Å °0.0031 Å °0.0163 Å °0.0443 Å °-0.0323 Å °0.005 Å °-0.0302 Å °

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