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- PDB-1vzm: OSTEOCALCIN FROM FISH ARGYROSOMUS REGIUS -

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Basic information

Entry
Database: PDB / ID: 1vzm
TitleOSTEOCALCIN FROM FISH ARGYROSOMUS REGIUS
ComponentsOSTEOCALCIN
KeywordsCALCIUM-BINDING PROTEIN / OSTEOCALCIN / BONE GLA PROTEIN / BGP / HYDROXYAPATITE / GAMMA CARBOXYL GLUTAMIC ACID / VITAMIN K / BONE / MINERALIZATION
Function / homology
Function and homology information


hydroxyapatite binding / structural constituent of bone / negative regulation of bone development / response to vitamin K / regulation of bone mineralization / type B pancreatic cell proliferation / bone mineralization / regulation of cellular response to insulin stimulus / hormone activity / bone development ...hydroxyapatite binding / structural constituent of bone / negative regulation of bone development / response to vitamin K / regulation of bone mineralization / type B pancreatic cell proliferation / bone mineralization / regulation of cellular response to insulin stimulus / hormone activity / bone development / cellular response to insulin stimulus / osteoblast differentiation / glucose homeostasis / : / calcium ion binding / extracellular region
Similarity search - Function
Osteocalcin / Osteocalcin/matrix Gla protein / 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 speciesARGYROSOMUS REGIUS (meagre)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsFrazao, C. / Simes, D.C. / Coelho, R. / Alves, D. / Williamson, M.K. / Price, P.A. / Cancela, M.L. / Carrondo, M.A.
Citation
Journal: Biochemistry / Year: 2005
Title: Structural Evidence of a Fourth Gla Residue in Fish Osteocalcin: Biological Implications
Authors: Frazao, C. / Simes, D.C. / Coelho, R. / Alves, D. / Williamson, M.K. / Price, P.A. / Cancela, M.L. / Carrondo, M.A.
#1: Journal: J.Bone Miner.Res. / Year: 2003
Title: Purification of Matrix Gla Protein from a Marine Teleost Fish, Argyrosomus Regius: Calcified Cartilage and not Bone as the Primary Site of Mgp Accumulation in Fish
Authors: Simes, D.C. / Williamson, M.K. / Ortiz-Delgado, J.B. / Viegas, C.S. / Price, P.A. / Cancela, M.L.
History
DepositionMay 21, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_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_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: OSTEOCALCIN
B: OSTEOCALCIN
C: OSTEOCALCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,33411
Polymers15,1403
Non-polymers1948
Water3,441191
1
A: OSTEOCALCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0712
Polymers5,0471
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OSTEOCALCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1194
Polymers5,0471
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: OSTEOCALCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1445
Polymers5,0471
Non-polymers974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.700, 48.700, 119.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.45312, -0.55241, 0.69966), (0.61561, -0.37375, -0.69378), (0.64475, 0.74509, 0.17071)23.09228, 52.35415, -18.95822
2given(0.07091, -0.73113, -0.67855), (-0.09366, -0.68213, 0.7252), (-0.99308, 0.01213, -0.11685)39.59732, 49.27197, 4.66851

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Components

#1: Protein/peptide OSTEOCALCIN


Mass: 5046.506 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ARGYROSOMUS REGIUS (meagre) / References: UniProt: Q800Y1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 294 K / pH: 8.5
Details: DROPS OF 1.5 MICRO-L OF PROTEIN SOLUTION, 10 MG/ML OSTEOCALCIN, 5 MM CACL2 AND 30 MM TRIS-HCL PH = 8, PLUS 1.5 MICRO-L OF WELL SOLUTION, MGCL2 0.2M, 30% PEG 4K AND TRIS-HCL 0.1M PH = 8.5, ...Details: DROPS OF 1.5 MICRO-L OF PROTEIN SOLUTION, 10 MG/ML OSTEOCALCIN, 5 MM CACL2 AND 30 MM TRIS-HCL PH = 8, PLUS 1.5 MICRO-L OF WELL SOLUTION, MGCL2 0.2M, 30% PEG 4K AND TRIS-HCL 0.1M PH = 8.5, WERE EQUILIBRATED AGAINST 500 ML OF WELL SOLUTION AT 21DEGREES C OVER 2-3 WEEKS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→39.75 Å / Num. obs: 32430 / % possible obs: 98.5 % / Redundancy: 22.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 34.8
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 5.2 / % possible all: 96.1

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→39.75 Å / Num. parameters: 11214 / Num. restraintsaints: 13702 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: EQUIVALENT BOND DISTANCES BETWEEN MAGNESIUM AND WATER-OXYGENS OR CARBOXYLATE-OXYGENS, WERE RESTRAINED TO CORRESPONDING AVERAGE DISTANCES, WITHOUT SPECIFIC TARGET VALUES 17 RESIDUES WERE ...Details: EQUIVALENT BOND DISTANCES BETWEEN MAGNESIUM AND WATER-OXYGENS OR CARBOXYLATE-OXYGENS, WERE RESTRAINED TO CORRESPONDING AVERAGE DISTANCES, WITHOUT SPECIFIC TARGET VALUES 17 RESIDUES WERE MODELED WITH ALTERNATING SIDE-CHAINS, AND 5 RESIDUES HAVE THEIR SIDE-CHAINS NOT TOTALLY INSIDE 1 SIGMA (0.07 ELECTRONS/A**3) ELECTRON DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 893 2.8 %SHELLS
all0.1916 32406 --
obs0.1916 -98.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 811 / Occupancy sum non hydrogen: 1193.75
Refinement stepCycle: LAST / Resolution: 1.4→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 8 191 1195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0243
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.083
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0.097

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