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- PDB-1gz2: Crystal structure of the Ovocleidin-17 a major protein of the Gal... -

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Basic information

Entry
Database: PDB / ID: 1gz2
TitleCrystal structure of the Ovocleidin-17 a major protein of the Gallus gallus eggshell calcified layer.
ComponentsOVOCLEIDIN-17
KeywordsSUGAR BINDING PROTEIN / STRUCTURAL PROTEIN / CTLD / EGGSHELL STRUCTURAL PROTEIN / PHOSPHOPROTEIN / SUGAR-BINDING PROTEIN / GLYCOPROTEIN / LECTIN
Function / homology
Function and homology information


shell calcification / organomineral extracellular matrix / biomineral tissue development / extracellular matrix protein binding / peptidoglycan binding / ion binding / antimicrobial humoral response / antigen binding / extracellular matrix / lipopolysaccharide binding ...shell calcification / organomineral extracellular matrix / biomineral tissue development / extracellular matrix protein binding / peptidoglycan binding / ion binding / antimicrobial humoral response / antigen binding / extracellular matrix / lipopolysaccharide binding / signaling receptor activity / antibacterial humoral response / carbohydrate binding / extracellular space / extracellular region
Similarity search - Function
Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsReyes-Grajeda, J.P. / Moreno, A. / Romero, A.
Citation
Journal: Protein Pept.Lett. / Year: 2002
Title: Crystallization and Preliminary X-Ray Analysis of Ovocleidin-17 a Major Protein of the Gallus Gallus Eggshell Calcified Layer
Authors: Reyes-Grajeda, J.P. / Jauregui-Zuniga, D. / Rodriguez-Romero, A. / Hernandez-Santoyo, A. / Bolanos-Garcia, V. / Moreno, A.
#1: Journal: Biochem.Mol.Biol.Int. / Year: 1999
Title: The Amino Acid Sequence of Ovocleidin 17, a Major Protein of the Avian Eggshell Calcified Layer
Authors: Mann, K. / Siedler, F.
#2: Journal: Embo J. / Year: 1996
Title: Crystal Structure of Human Lithostathine, the Pancreatic Inhibitor of Stone Formation
Authors: Bertrand, J.A. / Pignol, D. / Bernard, J.P. / Verdier, J.M. / Dagorn, J.C. / Fontecilla-Camps, J.C.
History
DepositionMay 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2003Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 13, 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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OVOCLEIDIN-17


Theoretical massNumber of molelcules
Total (without water)15,4041
Polymers15,4041
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.260, 58.260, 82.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein OVOCLEIDIN-17 / OC-17 OVOCLEIDIN


Mass: 15404.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / Tissue: EGGSHELL MATRIX / References: UniProt: Q9PRS8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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 Matthews: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growpH: 4.6 / Details: pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. obs: 26325 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIT

1lit


Resolution: 1.5→7.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1416513.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2582 9.9 %RANDOM
Rwork0.2 ---
obs0.2 26123 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.9893 Å2 / ksol: 0.484345 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20.83 Å20 Å2
2--2.27 Å20 Å2
3----4.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 153 1209
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.228 439 10.4 %
Rwork0.214 3782 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMSEP.TOP
X-RAY DIFFRACTION3SEP.PARAM

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