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- PDB-1dot: CRYSTALLOGRAPHIC STRUCTURE OF DUCK OVOTRANSFERRIN AT 2.3 ANGSTROM... -

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Basic information

Entry
Database: PDB / ID: 1dot
TitleCRYSTALLOGRAPHIC STRUCTURE OF DUCK OVOTRANSFERRIN AT 2.3 ANGSTROMS RESOLUTION
ComponentsDUCK OVOTRANSFERRIN
KeywordsIRON TRANSPORT PROTEIN
Function / homology
Function and homology information


iron ion transport / recycling endosome / antibacterial humoral response / early endosome / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II ...Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / alpha-L-fucopyranose / Ovotransferrin
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å
AuthorsRawas, A. / Muirhead, H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of diferric duck ovotransferrin at 2.35 A resolution.
Authors: Rawas, A. / Muirhead, H. / Williams, J.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary Crystallographic Studies on Duck Ovotransferrin
Authors: Rawas, A. / Moreton, K. / Muirhead, H. / Williams, J.
#2: Journal: Biochemistry / Year: 1988
Title: Molecular Structure of Serum Transferrin at 3.3 Angstroms Resolution
Authors: Bailey, S. / Evans, R.W. / Garratt, R.C. / Gorinsky, B. / Hasnain, S. / Horsburgh, C. / Jhoti, H. / Lindley, P.F. / Mydin, A. / Sarra, R. / Watson, J.L.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Structure of Human Lactoferrin at 3.2 Angstroms Resolution
Authors: Anderson, B.F. / Baker, H.M. / Dodson, E.J. / Norris, G.E. / Rumball, S.V. / Waters, J.M. / Baker, E.N.
History
DepositionAug 3, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Non-polymer description / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification ..._pdbx_database_status.process_site / _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.ndb_seq_num / _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.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.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET SHEETS N1, N2, C1, AND C2 ARE MIXED BETA SHEETS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUCK OVOTRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5708
Polymers75,7321
Non-polymers8387
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.600, 85.600, 178.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: PRO 2 - PRO 3 OMEGA = 149.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: PRO 3 - LYS 4 OMEGA = 132.22 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO 71
4: THR 279 - SER 280 OMEGA = 300.70 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: LYS 344 - ILE 345 OMEGA = 127.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DUCK OVOTRANSFERRIN / DOT


Mass: 75731.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anas platyrhynchos (mallard) / Cellular location: EGG WHITE / References: UniProt: P56410

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 322 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 291 K / pH: 5.8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-18 %PEG600011
20.01 Msodium acetate11
312-18 %(w/v)PEG600011

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorDetector: FILM / Date: 1986
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionNum. obs: 29846 / % possible obs: 90 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 2.35 Å / Lowest resolution: 10 Å / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
CCP4data collection
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
CCP4data reduction
X-PLORphasing
RefinementResolution: 2.35→10 Å / σ(F): 1
RfactorNum. reflection
Rfree0.32 -
Rwork0.23 -
obs0.23 27564
Displacement parametersBiso mean: 28.7 Å2
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5299 0 48 318 5665
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.7991.5
X-RAY DIFFRACTIONx_mcangle_it3.2762
X-RAY DIFFRACTIONx_scbond_it2.1922
X-RAY DIFFRACTIONx_scangle_it3.62.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_angle_d0.030.047
X-RAY DIFFRACTIONx_plane_restr0.030.026
X-RAY DIFFRACTIONx_chiral_restr0.120.197

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