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- PDB-4uww: Crystallographic Structure of the Intramineral Protein Struthical... -

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Basic information

Entry
Database: PDB / ID: 4uww
TitleCrystallographic Structure of the Intramineral Protein Struthicalcin from Struthio camelus Eggshell
ComponentsSTRUTHIOCALCIN-1
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


carbohydrate binding / extracellular region
Similarity search - Function
: / C-type lectin, conserved site / C-type lectin domain signature. / 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, conserved site / C-type lectin domain signature. / 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 speciesSTRUTHIO CAMELUS (African ostrich)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsRuiz, R.R. / Moreno, A. / Romero, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystal Structure of Struthiocalcin-1, an Intramineral Protein from Struthio Camelus Eggshell, in Two Different Crystal Forms.
Authors: Ruiz-Arellano, R.R. / Medrano, F.J. / Moreno, A. / Romero, A.
History
DepositionAug 14, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STRUTHIOCALCIN-1


Theoretical massNumber of molelcules
Total (without water)15,3771
Polymers15,3771
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.940, 72.600, 37.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein STRUTHIOCALCIN-1 / SCA-1


Mass: 15377.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STRUTHIO CAMELUS (African ostrich) / References: UniProt: P83514
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.97 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07153
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07153 Å / Relative weight: 1
ReflectionResolution: 1.44→44.31 Å / Num. obs: 28309 / % possible obs: 100 % / Observed criterion σ(I): 2.2 / Redundancy: 12.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.4
Reflection shellResolution: 4.54→44.31 Å / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 1.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→44.31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.371 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23156 1432 5.1 %RANDOM
Rwork0.21287 ---
obs0.21381 26876 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.44→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 0 74 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191138
X-RAY DIFFRACTIONr_bond_other_d0.0060.02988
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.8831544
X-RAY DIFFRACTIONr_angle_other_deg0.953.0052268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2325133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54322.90362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07115176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.026158
X-RAY DIFFRACTIONr_chiral_restr0.1310.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02307
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.362.511529
X-RAY DIFFRACTIONr_mcbond_other3.3012.503528
X-RAY DIFFRACTIONr_mcangle_it5.2153.758660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7893.053609
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.435→1.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 116 -
Rwork0.363 1904 -
obs--98.58 %

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