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- PDB-8i75: Crystal structure of decarboxylated osteocalcin at pH 2.0 -

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Basic information

Entry
Database: PDB / ID: 8i75
TitleCrystal structure of decarboxylated osteocalcin at pH 2.0
ComponentsOsteocalcin
KeywordsSTRUCTURAL PROTEIN / Ca-binding protein
Function / homology
Function and homology information


structural constituent of bone / hydroxyapatite binding / negative regulation of bone development / biomineral tissue development / regulation of testosterone biosynthetic process / response to vitamin K / type B pancreatic cell proliferation / regulation of bone mineralization / positive regulation of neurotransmitter secretion / regulation of cellular response to insulin stimulus ...structural constituent of bone / hydroxyapatite binding / negative regulation of bone development / biomineral tissue development / regulation of testosterone biosynthetic process / response to vitamin K / type B pancreatic cell proliferation / regulation of bone mineralization / positive regulation of neurotransmitter secretion / regulation of cellular response to insulin stimulus / bone development / brain development / hormone activity / cognition / osteoblast differentiation / cellular response to insulin stimulus / glucose homeostasis / learning or memory / calcium ion binding / extracellular region / cytoplasm
Similarity search - Function
Osteocalcin/matrix Gla protein / Osteocalcin / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues.
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsYokoyama, T. / Nabeshima, Y. / Obita, T. / Mizuguchi, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs Lett. / Year: 2023
Title: Structural and mutational analyses of decarboxylated osteocalcin provide insight into its adiponectin-inducing activity.
Authors: Mizuguchi, M. / Yokoyama, T. / Otani, T. / Kuribara, S. / Nabeshima, Y. / Obita, T. / Hirata, M. / Kawano, K.
History
DepositionJan 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Osteocalcin
B: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)8,4952
Polymers8,4952
Non-polymers00
Water1,06359
1
A: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)4,2481
Polymers4,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)4,2481
Polymers4,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.237, 42.237, 36.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein/peptide Osteocalcin / Bone Gla protein / BGP / Gamma-carboxyglutamic acid-containing protein


Mass: 4247.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: BGLAP / Production host: Escherichia coli (E. coli) / References: UniProt: P02820
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.94 Å3/Da / Density % sol: 36.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→23.21 Å / Num. obs: 72423 / % possible obs: 98.78 % / Redundancy: 4.85 % / CC1/2: 0.999 / Rrim(I) all: 0.039 / Net I/σ(I): 22.9
Reflection shellResolution: 1.33→1.38 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1437 / CC1/2: 0.89 / Rrim(I) all: 0.572

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→23.208 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 747 5.01 %
Rwork0.1847 --
obs0.187 14924 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.33→23.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms518 0 0 59 577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007532
X-RAY DIFFRACTIONf_angle_d0.777716
X-RAY DIFFRACTIONf_dihedral_angle_d28.308210
X-RAY DIFFRACTIONf_chiral_restr0.06866
X-RAY DIFFRACTIONf_plane_restr0.004100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.43080.22541470.17992781X-RAY DIFFRACTION98
1.4308-1.57480.2051490.15652846X-RAY DIFFRACTION100
1.5748-1.80260.19411510.15482855X-RAY DIFFRACTION100
1.8026-2.27070.20431500.19392848X-RAY DIFFRACTION100
2.2707-23.2080.25331500.19182847X-RAY DIFFRACTION97

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