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- PDB-2gyd: Complex of equine apoferritin with the H-diaziflurane photolabeli... -

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Basic information

Entry
Database: PDB / ID: 2gyd
TitleComplex of equine apoferritin with the H-diaziflurane photolabeling reagent
Componentsferritin L subunit
KeywordsMETAL BINDING PROTEIN / helical bundles / anesthetic / isoflurane
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
: / 2-(1,1-DIFLUOROETHOXY)-1,1,1-TRIFLUOROETHANE / : / Ferritin light chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.72 Å
AuthorsLoll, P.J. / Rossi, M.J. / Eckenhoff, R.
CitationJournal: Acs Chem.Biol. / Year: 2006
Title: Photoactive analogues of the haloether anesthetics provide high-resolution features from low-affinity interactions.
Authors: Xi, J. / Liu, R. / Rossi, M.J. / Yang, J. / Loll, P.J. / Dailey, W.P. / Eckenhoff, R.G.
History
DepositionMay 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_special_symmetry / 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.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_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_leaving_atom_flag / _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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN SER 27 reacts with H-diaziflurane to form the adduct 2-(1,1-DIFLUOROETHOXY)-1,1,1- ...HETEROGEN SER 27 reacts with H-diaziflurane to form the adduct 2-(1,1-DIFLUOROETHOXY)-1,1,1-TRIFLUOROETHANE (Ligand Code DFE)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ferritin L subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3549
Polymers19,4031
Non-polymers9518
Water3,297183
1
A: ferritin L subunit
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)488,493216
Polymers465,67024
Non-polymers22,823192
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 area97770 Å2
ΔGint-316 kcal/mol
Surface area134180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)181.890, 181.890, 181.890
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-1007-

CD

31A-1132-

HOH

41A-1158-

HOH

DetailsBiological unit is a 24-mer; see 1XZ1 for transformations required to create the 24-mer.

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Components

#1: Protein ferritin L subunit


Mass: 19402.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: horse spleen ferritin / Source: (natural) Equus caballus (horse) / References: GenBank: 62896483, UniProt: P02791*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-DFE / 2-(1,1-DIFLUOROETHOXY)-1,1,1-TRIFLUOROETHANE


Mass: 164.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5F5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M cadmium sulfate, 0.1 M HEPES, and 1.0 M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.72→37.13 Å / Num. all: 27676 / Num. obs: 27676 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.94 % / Rmerge(I) obs: 0.075 / Χ2: 0.69 / Net I/σ(I): 16.9 / Scaling rejects: 29232
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.72-1.7810.120.4322.82820825470.5193
1.78-1.8512.720.3594.23724726720.4497.7
1.85-1.9417.570.3577.25202227191.1199.9
1.94-2.0420.630.2818.16097327600.8100
2.04-2.1720.750.21610.35984527410.96100
2.17-2.3320.680.17312.96112027611.02100
2.33-2.5720.850.10914.26079027910.56100
2.57-2.9421.580.074216269527990.62100
2.94-3.7122.180.048296523128510.4299.9
3.71-37.1321.020.03540.46515430350.3699.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.4Ldata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
XTALVIEWrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1XZ1

1xz1


Resolution: 1.72→37.13 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.617 / SU ML: 0.054 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1409 5.1 %RANDOM
Rwork0.207 ---
all0.208 27673 --
obs0.208 27673 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.533 Å2
Refinement stepCycle: LAST / Resolution: 1.72→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 17 183 1554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221385
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.9771865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5775166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16324.32474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6415251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9311511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021043
X-RAY DIFFRACTIONr_nbd_refined0.2040.2679
X-RAY DIFFRACTIONr_nbtor_refined0.30.2970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.226
X-RAY DIFFRACTIONr_mcbond_it1.3971.5860
X-RAY DIFFRACTIONr_mcangle_it1.39521317
X-RAY DIFFRACTIONr_scbond_it2.5963586
X-RAY DIFFRACTIONr_scangle_it4.2624.5548
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 99 -
Rwork0.246 1774 -
obs-1873 92.63 %

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