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- PDB-1f35: CRYSTAL STRUCTURE OF MURINE OLFACTORY MARKER PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1f35
TitleCRYSTAL STRUCTURE OF MURINE OLFACTORY MARKER PROTEIN
ComponentsOLFACTORY MARKER PROTEIN
KeywordsSIGNALING PROTEIN / BETA / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


peptide binding / neurogenesis / sensory perception of smell / axon / neuronal cell body / signal transduction / nucleus / cytosol / cytoplasm
Similarity search - Function
Olfactory marker / Olfactory marker protein / Olfactory marker superfamily / Olfactory marker protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / Olfactory marker protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSmith, P.C. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The crystal structure of the olfactory marker protein at 2.3 A resolution.
Authors: Smith, P.C. / Firestein, S. / Hunt, J.F.
History
DepositionMay 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OLFACTORY MARKER PROTEIN
B: OLFACTORY MARKER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,77513
Polymers37,9842
Non-polymers79111
Water3,171176
1
A: OLFACTORY MARKER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5218
Polymers18,9921
Non-polymers5297
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OLFACTORY MARKER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2535
Polymers18,9921
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: OLFACTORY MARKER PROTEIN
hetero molecules

B: OLFACTORY MARKER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,77513
Polymers37,9842
Non-polymers79111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565x-y,-y+1,-z+1/31
Buried area3030 Å2
ΔGint-321 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.270, 87.270, 164.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer.

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Components

#1: Protein OLFACTORY MARKER PROTEIN


Mass: 18991.777 Da / Num. of mol.: 2
Mutation: M13(MSE), M25(MSE), M95(MSE), M115(MSE), M139(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: CDNA LIBRARY / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: Q64288
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 4.75 Å3/Da / Density % sol: 74.09 %
Description: 4 wavelengths used were: peak: 0.9786, edge: 0.9788, high energy remote: 0.9390, low energy remote: 1.078.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Zinc Acetate, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
2200 mMzinc acetate1reservoir
310 %(w/v)PEG80001reservoir
4100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9786, 0.9788, 0.9390, 1.078
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 20, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97881
30.9391
41.0781
ReflectionResolution: 2.2→40 Å / Num. all: 48740 / Num. obs: 35024 / % possible obs: 74 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 16.6 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 2.69
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.25 / Num. unique all: 2766 / % possible all: 71.8

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→100 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: X-PLOR 3.851
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1444 5 %RANDOM
Rwork0.21 ---
all-35024 --
obs-28907 88 %-
Displacement parametersBiso mean: 49.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0.48 Å20 Å2
2--0.17 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 15 176 2829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_improper_angle_d1.31
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.373 123 4.3 %
Rwork0.349 2766 -
obs--71.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parhcsdx_ace_cac.proparam19.sol
X-RAY DIFFRACTION2tophcsdx_ace_cac.protoph19.hoh
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31
LS refinement shell
*PLUS
Rfactor Rfree: 0.373 / % reflection Rfree: 4.3 % / Rfactor Rwork: 0.349

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