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- PDB-1ovt: REFINED CRYSTALLOGRAPHIC STRUCTURE OF HEN OVOTRANSFERRIN AT 2.4 A... -

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Entry
Database: PDB / ID: 1ovt
TitleREFINED CRYSTALLOGRAPHIC STRUCTURE OF HEN OVOTRANSFERRIN AT 2.4 ANGSTROMS RESOLUTION
ComponentsOVOTRANSFERRIN
KeywordsIRON TRANSPORT PROTEIN
Function / homology
Function and homology information


organomineral extracellular matrix / iron ion transmembrane transport / antimicrobial humoral response / ferric iron binding / acute-phase response / iron ion transport / recycling endosome / antibacterial humoral response / response to lipopolysaccharide / intracellular iron ion homeostasis ...organomineral extracellular matrix / iron ion transmembrane transport / antimicrobial humoral response / ferric iron binding / acute-phase response / iron ion transport / recycling endosome / antibacterial humoral response / response to lipopolysaccharide / intracellular iron ion homeostasis / early endosome / iron ion binding / response to xenobiotic stimulus / extracellular space / 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 / : / Ovotransferrin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsKurokawa, H. / Mikami, B. / Hirose, M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of diferric hen ovotransferrin at 2.4 A resolution.
Authors: Kurokawa, H. / Mikami, B. / Hirose, M.
#1: Journal: Biochemistry / Year: 1993
Title: Structural Evidence for a Ph Sensitive Di-Lysine Trigger in the Hen Ovotransferrin N-Lobe: Implications for Transferrin Iron Release
Authors: Dewan, J.C. / Mikami, B. / Hirose, M. / Sacchettini, J.C.
#2: Journal: J.Biochem.(Tokyo) / Year: 1990
Title: Crystallization of N-Terminal Lobe of Ovotransferrin
Authors: Mikami, B. / Hirose, M.
History
DepositionApr 28, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _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 / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET THERE IS ONE BIFURCATED SHEET IN EACH OF THE TWO LOBES OF OVOTRANSFERRIN. SHEET S1 IS ...SHEET THERE IS ONE BIFURCATED SHEET IN EACH OF THE TWO LOBES OF OVOTRANSFERRIN. SHEET S1 IS PRESENTED AS SHEETS S1A, S1B, AND S1C ON SHEET RECORDS BELOW. NOTE THAT STRANDS 4 OF S1A AND 3 OF S1B ARE IDENTICAL, STRANDS 1 OF S1B AND 3 OF S1C ARE IDENTICAL, AND STRANDS 2 OF S1B AND 4 OF S1C ARE IDENTICAL. SHEET S2 IS PRESENTED AS SHEETS S2A, S2B, AND S2C ON SHEET RECORDS BELOW. NOTE THAT STRANDS 4 OF S2A AND 3 OF S2B ARE IDENTICAL, STRANDS 1 OF S2B AND 3 OF S2C ARE IDENTICAL, AND STRANDS 2 OF S2B AND 4 OF S2C ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OVOTRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1615
Polymers75,9291
Non-polymers2324
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.190, 60.940, 90.240
Angle α, β, γ (deg.)90.00, 83.95, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 71 / 2: CIS PROLINE - PRO 287
3: SER 339 - PRO 340 OMEGA = 143.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ARG 427 - PRO 428 OMEGA = 238.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: PRO 509 - PRO 510 OMEGA = 250.41 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein OVOTRANSFERRIN / CONALBUMIN


Mass: 75929.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DIFERRIC FORM / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02789
#2: Chemical ChemComp-FE / FE (III) ION


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


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


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.9 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mg/mlprotein11
20.02 Msodium acetate11
320 %(w/v)PEG600011

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Data collection

DetectorDate: Dec 3, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 28473 / % possible obs: 87 % / Redundancy: 3.2 %
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 11 Å / Observed criterion σ(F): 2 / Num. measured all: 61204

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Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.4→11 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.171 -
obs0.171 19714
Displacement parametersBiso mean: 24 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5284 0 10 132 5426
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.28
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_deg1.26

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