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- PDB-4xav: Crystal structure of olfactomedin domain from gliomedin -

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Basic information

Entry
Database: PDB / ID: 4xav
TitleCrystal structure of olfactomedin domain from gliomedin
ComponentsGliomedin
KeywordsCELL ADHESION / beta propeller / 5 bladed propeller / olfactomedin
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 / 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
PHOSPHATE ION / Gliomedin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.052 Å
AuthorsHill, S.E. / Nguyen, E. / Lieberman, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: Plos One / Year: 2015
Title: Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies.
Authors: Hill, S.E. / Donegan, R.K. / Nguyen, E. / Desai, T.M. / Lieberman, R.L.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _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.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
Revision 1.4Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gliomedin
B: Gliomedin
C: Gliomedin
D: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,76319
Polymers123,6354
Non-polymers1,12815
Water14,448802
1
A: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2145
Polymers30,9091
Non-polymers3054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1164
Polymers30,9091
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1224
Polymers30,9091
Non-polymers2133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Gliomedin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3126
Polymers30,9091
Non-polymers4035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.164, 140.643, 78.152
Angle α, β, γ (deg.)90.00, 106.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gliomedin / Cancer-related gene liver 2 protein / CRG-L2


Mass: 30908.846 Da / Num. of mol.: 4 / Fragment: UNP residues 279-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gldn, Crgl2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BMF8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: phosphate citrate pH 5.5 PEG 600

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→44.65 Å / Num. obs: 59953 / % possible obs: 98.2 % / Redundancy: 5.2 % / Net I/σ(I): 9.05

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000phasing
PHENIXmodel building
PHENIXphasing
RefinementResolution: 2.052→44.646 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1998 3.34 %
Rwork0.1662 --
obs0.1678 59848 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.052→44.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7900 0 62 802 8764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058155
X-RAY DIFFRACTIONf_angle_d0.92411039
X-RAY DIFFRACTIONf_dihedral_angle_d13.0742890
X-RAY DIFFRACTIONf_chiral_restr0.0371188
X-RAY DIFFRACTIONf_plane_restr0.0041388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.052-2.10310.23431380.17173920X-RAY DIFFRACTION94
2.1031-2.15990.26851440.18194082X-RAY DIFFRACTION97
2.1599-2.22350.23151390.18274120X-RAY DIFFRACTION98
2.2235-2.29520.25311380.18034106X-RAY DIFFRACTION98
2.2952-2.37730.23121480.17834184X-RAY DIFFRACTION98
2.3773-2.47240.24221410.18514135X-RAY DIFFRACTION98
2.4724-2.58490.27781450.18354090X-RAY DIFFRACTION98
2.5849-2.72120.2741390.18594136X-RAY DIFFRACTION98
2.7212-2.89170.23351430.18534150X-RAY DIFFRACTION99
2.8917-3.11490.24551480.18374154X-RAY DIFFRACTION99
3.1149-3.42830.18911440.15584188X-RAY DIFFRACTION99
3.4283-3.92410.1841430.1464203X-RAY DIFFRACTION99
3.9241-4.94290.14461470.13144186X-RAY DIFFRACTION99
4.9429-44.65610.20291410.17514196X-RAY DIFFRACTION98

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