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- PDB-1job: Crystal Structure of Murine Olfactory Marker Protein in Spacegrou... -

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Basic information

Entry
Database: PDB / ID: 1job
TitleCrystal Structure of Murine Olfactory Marker Protein in Spacegroup P3121
ComponentsOlfactory Marker Protein
KeywordsSIGNALING PROTEIN / Beta Clamshell
Function / homology
Function and homology information


neurogenesis / peptide binding / sensory perception of smell / axon / neuronal cell body / signal transduction / nucleus / cytoplasm / cytosol
Similarity search - Function
Olfactory marker / Olfactory marker protein / Olfactory marker superfamily / Olfactory marker protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Olfactory marker protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSmith, P. / Hunt, J.F.
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
DepositionJul 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Aug 16, 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 / 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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Olfactory Marker Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1507
Polymers18,7571
Non-polymers3926
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Olfactory Marker Protein
hetero molecules

A: Olfactory Marker Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,30014
Polymers37,5152
Non-polymers78512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2640 Å2
ΔGint-305 kcal/mol
Surface area17520 Å2
MethodPISA, PQS
3
A: Olfactory Marker Protein
hetero molecules

A: Olfactory Marker Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,30014
Polymers37,5152
Non-polymers78512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area1300 Å2
ΔGint-305 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.327, 86.327, 71.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-303-

ZN

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Components

#1: Protein Olfactory Marker Protein


Mass: 18757.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: OMP / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q64288
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 4.1 Å3/Da / Density % sol: 70.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Zinc Acetate, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: unknown / Details: unpublished structure

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.276 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 29, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.276 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 12201 / Num. obs: 11701 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 19.31 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 23.1 / Net I/σ(I): 12.6
Reflection shellResolution: 2.4→2.49 Å / Num. unique all: 152

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F35

1f35


Resolution: 2.4→40 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 569 4.9 %RANDOM
Rwork0.234 ---
obs0.234 11701 94.4 %-
all-12270 --
Displacement parametersBiso mean: 51.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å2-2.38 Å20 Å2
2---1.09 Å20 Å2
3---2.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 0 6 158 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_improper_angle_d2.32
X-RAY DIFFRACTIONx_mcbond_it2.921.5
X-RAY DIFFRACTIONx_mcangle_it4.162
X-RAY DIFFRACTIONx_scbond_it42
X-RAY DIFFRACTIONx_scangle_it5.862.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.363 61 5.8 %
Rwork0.396 995 -
obs--86.4 %

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