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- PDB-4mzz: Crystal structure of Bovine 3 Glu-Osteocalcin. -

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Basic information

Entry
Database: PDB / ID: 4mzz
TitleCrystal structure of Bovine 3 Glu-Osteocalcin.
ComponentsOsteocalcin
KeywordsSTRUCTURAL PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


hydroxyapatite binding / structural constituent of bone / negative regulation of bone development / biomineral tissue development / regulation of testosterone biosynthetic process / response to vitamin K / regulation of bone mineralization / type B pancreatic cell proliferation / positive regulation of neurotransmitter secretion / regulation of cellular response to insulin stimulus ...hydroxyapatite binding / structural constituent of bone / negative regulation of bone development / biomineral tissue development / regulation of testosterone biosynthetic process / response to vitamin K / regulation of bone mineralization / type B pancreatic cell proliferation / positive regulation of neurotransmitter secretion / regulation of cellular response to insulin stimulus / hormone activity / bone development / brain development / cognition / cellular response to insulin stimulus / osteoblast differentiation / glucose homeostasis / learning or memory / calcium ion binding / extracellular region / cytoplasm
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsMalashkevich, V.N. / Dowd, T.L. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Biochemistry / Year: 2013
Title: X-ray crystal structure of bovine 3 Glu-osteocalcin.
Authors: Malashkevich, V.N. / Almo, S.C. / Dowd, T.L.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)7,8052
Polymers7,8052
Non-polymers00
Water54030
1
A: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)3,9021
Polymers3,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)3,9021
Polymers3,9021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.761, 42.761, 37.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 1 / Auth seq-ID: 17 - 46 / Label seq-ID: 1 - 30

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsmonomeric

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Components

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


Mass: 3902.307 Da / Num. of mol.: 2 / Fragment: UNP residues 52-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P02820
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE STARTING SEQUENCE OF THE EXPERIMENT WAS YLDHWLGA(O)APYPDPLEPKREVCELNPDCDELADHIGFQEAYRRFYGPV ...THE STARTING SEQUENCE OF THE EXPERIMENT WAS YLDHWLGA(O)APYPDPLEPKREVCELNPDCDELADHIGFQEAYRRFYGPV WHERE (O) INDICATES OXYPROLINE. AUTHOR STATES THAT FIRST 16 RESIDUES ARE NOT VISIBLE IN ANY OF THE SOLVED STRUCTURES, PROBABLY DUE TO PROTEOLYSIS BEFORE OR DURING CRYSTALLIZATION

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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: 2.34 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5 M ammonium sulfate, 0.1 M Bis-Tris propane:NaOH, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.504
11K, H, -L20.496
ReflectionResolution: 1.88→50 Å / Num. obs: 5664 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.065 / Χ2: 2.252 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.88-1.916.50.7242781.231198.9
1.91-1.9570.6372931.2531100
1.95-1.987.30.4832741.2971100
1.98-2.037.20.4652851.441100
2.03-2.077.40.3342691.5251100
2.07-2.127.30.2422881.5631100
2.12-2.177.30.2112761.6171100
2.17-2.237.40.1892941.7311100
2.23-2.297.40.1732671.9481100
2.29-2.377.40.1182892.0551100
2.37-2.457.30.1212712.1451100
2.45-2.557.30.1012882.31100
2.55-2.677.30.0942782.5561100
2.67-2.817.20.0822822.6591100
2.81-2.987.20.0722912.8481100
2.98-3.217.10.062833.2921100
3.21-3.546.90.0582843.5311100
3.54-4.056.60.0542823.9821100
4.05-5.16.50.0412953.342199.7
5.1-506.30.0382973.031198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q8H

1q8h


Resolution: 1.88→42.76 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2628 / WRfactor Rwork: 0.1919 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8119 / SU B: 6.316 / SU ML: 0.088 / SU R Cruickshank DPI: 0.0296 / SU Rfree: 0.0318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 258 4.6 %RANDOM
Rwork0.1743 ---
obs0.1775 5647 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.96 Å2 / Biso mean: 41.1024 Å2 / Biso min: 21.35 Å2
Baniso -1Baniso -2Baniso -3
1--13.41 Å2-0 Å2-0 Å2
2---13.41 Å2-0 Å2
3---26.82 Å2
Refinement stepCycle: LAST / Resolution: 1.88→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms525 0 0 30 555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019540
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.965728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.707561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42423.88936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9111586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.703156
X-RAY DIFFRACTIONr_chiral_restr0.0990.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021446
X-RAY DIFFRACTIONr_mcbond_it1.9316.572250
X-RAY DIFFRACTIONr_mcangle_it3.114309
X-RAY DIFFRACTIONr_scbond_it2.4177.562290
Refine LS restraints NCSNumber: 52 / Type: TIGHT THERMAL / Rms dev position: 1.96 Å / Weight position: 10
LS refinement shellResolution: 1.883→1.931 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 6 -
Rwork0.176 406 -
all-412 -
obs--99.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.9152-0.5977-2.79053.744-0.18623.5685-0.09530.09540.0088-0.0543-0.1241-0.19180.04360.00460.21940.0580.00150.00980.06870.02120.028818.7948-11.2355-2.5137
21.5338-1.1110.68638.31262.29824.6348-0.1977-0.09020.13350.2301-0.07480.0488-0.0918-0.06840.27250.0842-0.0031-0.02620.055-0.0080.02359.8282-2.49848.3067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 47
2X-RAY DIFFRACTION2B17 - 48

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