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- PDB-4d7c: Monoclinic crystal form of the extracellular olfactomedin domain ... -

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Basic information

Entry
Database: PDB / ID: 4d7c
TitleMonoclinic crystal form of the extracellular olfactomedin domain from gliomedin
ComponentsGLIOMEDIN
KeywordsSIGNALING PROTEIN / MYELIN / BETA-PROPELLER
Function / homology
Function and homology information


clustering of voltage-gated sodium channels / protein binding involved in heterotypic cell-cell adhesion / microvillus organization / collagen trimer / axon / cell surface / signal transduction / extracellular space / plasma membrane
Similarity search - Function
: / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHan, H. / Kursula, P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Olfactomedin Domain from Gliomedin is a Beta-Propeller with Unique Structural Properties.
Authors: Han, H. / Kursula, P.
History
DepositionNov 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_status.status_code_sf / _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.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.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.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_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

Downloads & links

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Assembly

Deposited unit
A: GLIOMEDIN
B: GLIOMEDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9174
Polymers64,8712
Non-polymers462
Water10,106561
1
A: GLIOMEDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4582
Polymers32,4361
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLIOMEDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4582
Polymers32,4361
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.550, 141.700, 46.030
Angle α, β, γ (deg.)90.00, 110.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLIOMEDIN


Mass: 32435.500 Da / Num. of mol.: 2 / Fragment: OLFACTOMEDIN DOMAIN, UNP RESIDUES 260-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q80WL1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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 % sol: 40 % / Description: NONE
Crystal growDetails: 100 MM SODIUM CITRATE PH 5.5, 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 78451 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.4
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.3 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D77

4d77


Resolution: 1.45→43.084 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 1565 2 %
Rwork0.1734 --
obs0.1742 78443 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→43.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 2 561 4536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154208
X-RAY DIFFRACTIONf_angle_d1.0295708
X-RAY DIFFRACTIONf_dihedral_angle_d12.9071533
X-RAY DIFFRACTIONf_chiral_restr0.066622
X-RAY DIFFRACTIONf_plane_restr0.006724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.49680.3361370.30656908X-RAY DIFFRACTION97
1.4968-1.55030.33051510.2686912X-RAY DIFFRACTION98
1.5503-1.61240.29471310.23476916X-RAY DIFFRACTION98
1.6124-1.68580.25831450.21226943X-RAY DIFFRACTION99
1.6858-1.77460.25621420.19877034X-RAY DIFFRACTION99
1.7746-1.88580.23611400.17316975X-RAY DIFFRACTION99
1.8858-2.03140.20741470.15876974X-RAY DIFFRACTION99
2.0314-2.23590.15741380.14837009X-RAY DIFFRACTION99
2.2359-2.55940.20371430.15237062X-RAY DIFFRACTION100
2.5594-3.22440.18571470.16247034X-RAY DIFFRACTION100
3.2244-43.10270.19321440.15597111X-RAY DIFFRACTION99

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