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- PDB-1jnf: Rabbit serum transferrin at 2.6 A resolution. -

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Basic information

Entry
Database: PDB / ID: 1jnf
TitleRabbit serum transferrin at 2.6 A resolution.
Componentsserotransferrin
KeywordsMETAL BINDING PROTEIN / beta-alpha protein / bilobal / iron transport
Function / homology
Function and homology information


ferric iron binding / iron ion transport / intracellular iron ion homeostasis / extracellular space
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-like domain / Transferrin / 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-like domain / Transferrin / 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 / SYNCHROTRON / Resolution: 2.6 Å
AuthorsHall, D.R. / Hadden, J.M. / Leonard, G.A. / Bailey, S. / Neu, M. / Winn, M. / Lindley, P.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The crystal and molecular structures of diferric porcine and rabbit serum transferrins at resolutions of 2.15 and 2.60 A, respectively.
Authors: Hall, D.R. / Hadden, J.M. / Leonard, G.A. / Bailey, S. / Neu, M. / Winn, M. / Lindley, P.F.
History
DepositionJul 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1586
Polymers74,8911
Non-polymers2675
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.190, 127.190, 144.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein serotransferrin


Mass: 74891.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: serum / References: UniProt: P19134
#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 279 K / Method: batch crystallisation / pH: 5.4
Details: 0.01M Tris/HCl, acetic acid or HCl, pH 5.4, Batch crystallisation, temperature 279K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1993 / Details: Pt-coated quartz
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 36323 / Num. obs: 36323 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.9
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2290 / % possible all: 85.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
MLPHAREphasing
REFMAC5refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementStarting model: Structure at 3.3 A determined by MIR

Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.141 / SU ML: 0.223 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.323 / ESU R Free: 0.236 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1808 5 %RANDOM
Rwork0.185 ---
all0.187 34433 --
obs0.187 34433 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: babinet model with mask
Displacement parametersBiso mean: 44.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 0 11 206 5433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215357
X-RAY DIFFRACTIONr_bond_other_d0.0010.024692
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.9637251
X-RAY DIFFRACTIONr_angle_other_deg0.933311010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.73673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.10715956
X-RAY DIFFRACTIONr_chiral_restr0.1210.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026001
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021053
X-RAY DIFFRACTIONr_nbd_refined0.2540.31386
X-RAY DIFFRACTIONr_nbd_other0.2350.34948
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.5431
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1640.511
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.34
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.314
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0771.53357
X-RAY DIFFRACTIONr_mcangle_it2.01625363
X-RAY DIFFRACTIONr_scbond_it2.70432000
X-RAY DIFFRACTIONr_scangle_it4.6324.51888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 118 -
Rwork0.237 --
obs-2172 86.12 %

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