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- PDB-1h76: The crystal structure of diferric porcine serum transferrin -

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Basic information

Entry
Database: PDB / ID: 1h76
TitleThe crystal structure of diferric porcine serum transferrin
ComponentsSEROTRANSFERRIN
KeywordsIRON TRANSPORT / GLYCOPROTEIN / METAL-BINDING
Function / homology
Function and homology information


ferric iron binding / recycling endosome / antibacterial humoral response / iron ion transport / 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-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 speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 2.60A, Respectively
Authors: Hall, D.R. / Hadden, J.M. / Leonard, G.A. / Bailey, S. / Neu, M. / Winn, M. / Lindley, P.F.
History
DepositionJul 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 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: SEROTRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5216
Polymers77,0681
Non-polymers4535
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)223.770, 44.890, 78.860
Angle α, β, γ (deg.)90.00, 105.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SEROTRANSFERRIN / SIDEROPHILIN / BETA-1-METAL BINDING GLOBULIN


Mass: 77067.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BLOOD / Source: (natural) SUS SCROFA (pig) / References: UniProt: P09571
#2: Chemical ChemComp-CO3 / CARBONATE ION


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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: 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.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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 / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Temperature: 277 K / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1120 mg/mlprotein11in water
220 %(w/v)PEG400011
30.2 M11Li2SO4
40.1 MTris-HCl11

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.15→23.3 Å / Num. obs: 41503 / % possible obs: 96 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.7
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 8.1 / % possible all: 97.4
Reflection
*PLUS
Lowest resolution: 23.31 Å / % possible obs: 96 % / Num. measured all: 145143
Reflection shell
*PLUS
% possible obs: 97.4 %

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
DENZOdata reduction
XDISPdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 0TFD

Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.425 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE SIDE CHAINS OF THE FOLLOWING RESIDUES WERE DISORDERED AND TRUNCATED AT THE C-BETA: GLN A 3, GLU A 342, LYS A 345, GLU A 421 THE SIDE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE SIDE CHAINS OF THE FOLLOWING RESIDUES WERE DISORDERED AND TRUNCATED AT THE C-BETA: GLN A 3, GLU A 342, LYS A 345, GLU A 421 THE SIDE CHAINS OF THE FOLLOWING RESIDUES WERE FOUND IN DUAL CONFORMATIONS: ASP A 202, TYR A 399, ASP A 444, ASN A 478, ASP A 544
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2001 5 %RANDOM
Rwork0.136 ---
obs-38011 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5233 0 24 494 5751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0215400
X-RAY DIFFRACTIONr_bond_other_d0.0010.024660
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.9611.9537307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.364310928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026082
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021069
X-RAY DIFFRACTIONr_nbd_refined0.2240.31148
X-RAY DIFFRACTIONr_nbd_other0.2120.34476
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1920.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5492
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3890.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3131.53369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42425377
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3932031
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5934.51930
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.217 144
Rwork0.136 2829
Software
*PLUS
Name: REFMAC / Version: 5.0.32 18/01/2001 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.136 / Rfactor Rfree: 0.182 / Rfactor Rwork: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.89
X-RAY DIFFRACTIONp_plane_restr0.008
X-RAY DIFFRACTIONp_chiral_restr0.113

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