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- PDB-1tfd: HIGH-RESOLUTION X-RAY STUDIES ON RABBIT SERUM TRANSFERRIN: PRELIM... -

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Basic information

Entry
Database: PDB / ID: 1tfd
TitleHIGH-RESOLUTION X-RAY STUDIES ON RABBIT SERUM TRANSFERRIN: PRELIMINARY STRUCTURE ANALYSIS OF THE N-TERMINAL HALF-MOLECULE AT 2.3 ANGSTROMS RESOLUTION
ComponentsTRANSFERRIN
KeywordsIRON TRANSPORT PROTEIN
Function / homology
Function and homology information


ferric iron binding / iron ion transport / recycling endosome / antibacterial humoral response / intracellular iron ion homeostasis / early endosome / extracellular space / plasma membrane
Similarity search - Function
Serotransferrin, mammalian / 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 ...Serotransferrin, mammalian / 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 / : / Serotransferrin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSarra, R. / Lindley, P.F.
Citation
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.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1986
Title: Preliminary X-Ray Data for an N-Terminal Fragment of Rabbit Serum Transferrin
Authors: Sarra, R. / Lindley, P.F.
#3: Journal: J.Mol.Biol. / Year: 1976
Title: Crystallization and Preliminary X-Ray Investigation of Rabbit Plasma Transferrin
Authors: Al-Hilal, D. / Baker, E. / Carlisle, C.H. / Gorinsky, B. / Horsburgh, R.C. / Lindley, P.F. / Moss, D.S. / Schneider, H. / Stimpson, R.
History
DepositionAug 16, 1990Processing site: BNL
Revision 1.0Apr 15, 1993Provider: 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_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_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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6643
Polymers33,5481
Non-polymers1162
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.060, 67.060, 138.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: THE DISULFIDE BRIDGE NORMALLY PRESENT BETWEEN RESIDUES CYS 137 AND CYS 331 COULD NOT BE BUILT BECAUSE RESIDUE 331 IS NOT PRESENT IN THIS STRUCTURE.

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Components

#1: Protein TRANSFERRIN


Mass: 33548.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P19134
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal grow
*PLUS
Temperature: 279 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 %(w/v)protein1drop
225 %(w/v)PEG60001drop
350 mMPIPES disodium1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 15395 / % possible obs: 85.8 % / Rmerge(I) obs: 0.061

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.225 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 5 0 2285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d

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