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- PDB-1ovb: THE MECHANISM OF IRON UPTAKE BY TRANSFERRINS: THE STRUCTURE OF AN... -

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Basic information

Entry
Database: PDB / ID: 1ovb
TitleTHE MECHANISM OF IRON UPTAKE BY TRANSFERRINS: THE STRUCTURE OF AN 18KD NII-DOMAIN FRAGMENT AT 2.3 ANGSTROMS RESOLUTION
ComponentsOVOTRANSFERRIN
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 / : / Ovotransferrin
Similarity search - Component
Biological speciesAnas sp. (bird)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsKuser, P. / Lindley, P. / Sarra, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: The mechanism of iron uptake by transferrins: the structure of an 18 kDa NII-domain fragment from duck ovotransferrin at 2.3 A resolution.
Authors: Lindley, P.F. / Bajaj, M. / Evans, R.W. / Garratt, R.C. / Hasnain, S.S. / Jhoti, H. / Kuser, P. / Neu, M. / Patel, K. / Sarra, R. / Strange, R. / Walton, A.
#1: Journal: J.Inorg.Biochem. / Year: 1992
Title: New Perspectives on the Structure and Function of Transferrins
Authors: Baker, E.N. / Lindley, P.F.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: High-Resolution X-Ray Studies on Rabbit Serum Transferrin-Preliminary Structure Analysis of the N-Terminal Half-Molecule at 2.3 Angstroms Resolution
Authors: Sarra, R. / Garratt, R. / Gorinsky, B. / Jhoti, H. / Lindley, P.
#3: 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.
History
DepositionOct 5, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: OVOTRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5453
Polymers17,4291
Non-polymers1162
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.500, 41.500, 81.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Atom site foot note1: GLY 104 - THR 105 OMEGA ANGLE = 137.204 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA 126 - GLY 127 OMEGA ANGLE = 217.267 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ILE 141 - GLU 142 OMEGA ANGLE = 143.256 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: GLU 142 - SER 143 OMEGA ANGLE = 242.000 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: GLU 224 - LEU 225 OMEGA ANGLE = 211.241 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein OVOTRANSFERRIN


Mass: 17428.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas sp. (bird) / References: UniProt: P56410
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IS THAT DETERMINED BY THE AUTHORS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
240 %(v/v)MPD1reservoir
350 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 6535 / % possible obs: 90.1 % / Num. measured all: 13822 / Rmerge(I) obs: 0.044

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→7 Å /
RfactorNum. reflection
Rwork0.195 -
obs0.195 6555
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 5 106 1331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 7 Å / Num. reflection obs: 6555 / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_angle_d0.050.011
X-RAY DIFFRACTIONx_plane_restr0.020.003
X-RAY DIFFRACTIONx_chiral_restr0.0250.013
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.44 Å / Total num. of bins used: 6 / Num. reflection obs: 1098 / Rfactor obs: 0.338

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