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- PDB-3l9b: Crystal Structure of Rat Otoferlin C2A -

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Basic information

Entry
Database: PDB / ID: 3l9b
TitleCrystal Structure of Rat Otoferlin C2A
ComponentsOtoferlin
KeywordsMEMBRANE PROTEIN / Otoferlin / C2-domain / beta-sheets / Cell membrane / Synaptic vesicle / Hearing / Membrane / Synapse / Transmembrane
Function / homology
Function and homology information


AP-2 adaptor complex binding / plasma membrane organization / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / basal part of cell / synaptic vesicle priming / cochlea development / synaptic vesicle exocytosis / presynaptic active zone membrane / cell projection / sensory perception of sound ...AP-2 adaptor complex binding / plasma membrane organization / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / basal part of cell / synaptic vesicle priming / cochlea development / synaptic vesicle exocytosis / presynaptic active zone membrane / cell projection / sensory perception of sound / synaptic vesicle membrane / apical part of cell / basolateral plasma membrane / membrane => GO:0016020 / Golgi membrane / calcium ion binding / protein-containing complex binding / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Otoferlin / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain / Ferlin, fifth C2 domain / Ferlin, sixth C2 domain ...Otoferlin / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain / Ferlin, fifth C2 domain / Ferlin, sixth C2 domain / Ferlin, first C2 domain / FerB (NUC096) domain / FerI (NUC094) domain / Ferlin C-terminus / FerB / FerI / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHelfmann, S. / Neumann, P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The crystal structure of the C2A domain of otoferlin reveals an unconventional top loop region.
Authors: Helfmann, S. / Neumann, P. / Tittmann, K. / Moser, T. / Ficner, R. / Reisinger, E.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Nov 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Otoferlin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4372
Polymers16,4131
Non-polymers241
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.300, 100.300, 30.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-125-

MG

21A-242-

HOH

31A-248-

HOH

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Components

#1: Protein Otoferlin / / Fer-1-like protein 2


Mass: 16412.512 Da / Num. of mol.: 1 / Fragment: C2A domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fer1l2, Otof / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ERC5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, MgCl2, pH 8.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 13, 2009
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 10992 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.01 % / Biso Wilson estimate: 31.179 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.073 / Net I/σ(I): 15.03
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 2.93 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 4473 / Num. unique all: 4473 / Num. unique obs: 1522 / Rsym value: 0.577 / % possible all: 99.3

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Phasing

Phasing MRRfactor: 57.08 / Model details: Phaser MODE: MR_AUTO / Packing: 0
Highest resolutionLowest resolution
Rotation2.6 Å24.83 Å
Translation2.6 Å24.83 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DSY

1dsy


Resolution: 1.95→24.937 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.829 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement in phenix.refine using automatic procedure to determine the weights between X-ray target and stereochemistry/ADP restraints, mask optimisation
RfactorNum. reflection% reflectionSelection details
Rfree0.229 551 5.01 %RANDOM
Rwork0.181 ---
all0.3451 ---
obs0.183 10990 98.41 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.363 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 103.32 Å2 / Biso mean: 32.871 Å2 / Biso min: 12.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.227 Å2-0 Å20 Å2
2---1.227 Å20 Å2
3---2.454 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-8 Å
Luzzati sigma a0.27 Å1.2 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 1 143 1159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061059
X-RAY DIFFRACTIONf_angle_d0.9811434
X-RAY DIFFRACTIONf_chiral_restr0.073167
X-RAY DIFFRACTIONf_plane_restr0.003186
X-RAY DIFFRACTIONf_dihedral_angle_d17.992392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.1460.31380.2362598273699
2.146-2.4570.2541350.2032576271199
2.457-3.0940.2521380.1832615275399
3.094-24.9390.1961400.1592650279097
Refinement TLS params.Method: refined / Origin x: -11.4466 Å / Origin y: -3.1639 Å / Origin z: -1.4974 Å
111213212223313233
T0.1643 Å2-0.0174 Å2-0.0434 Å2-0.1096 Å20.0088 Å2--0.1526 Å2
L2.0604 °20.8731 °2-0.4101 °2-1.5969 °20.0373 °2--1.6557 °2
S-0.0395 Å °0.0495 Å °0.1597 Å °-0.1033 Å °-0.0182 Å °0.1978 Å °-0.2324 Å °0.0137 Å °0.0604 Å °
Refinement TLS groupSelection details: chain A

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