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- PDB-2o7u: Crystal structure of K206E/K296E mutant of the N-terminal half mo... -

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Basic information

Entry
Database: PDB / ID: 2o7u
TitleCrystal structure of K206E/K296E mutant of the N-terminal half molecule of human transferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Human transferrin / Iron binding protein / Dilysine pair
Function / homology
Function and homology information


iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion ...iron chaperone activity / transferrin receptor binding / Transferrin endocytosis and recycling / basal part of cell / endocytic vesicle / clathrin-coated pit / ferric iron binding / basal plasma membrane / osteoclast differentiation / cellular response to iron ion / Post-translational protein phosphorylation / iron ion transport / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / regulation of iron ion transport / ferrous iron binding / HFE-transferrin receptor complex / recycling endosome / regulation of protein stability / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / antibacterial humoral response / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Platelet degranulation / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / cytoplasmic vesicle / secretory granule lumen / blood microparticle / vesicle / transmembrane transporter binding / intracellular iron ion homeostasis / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / perinuclear region of cytoplasm / enzyme binding / cell surface / extracellular space / extracellular exosome / extracellular region / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBaker, H.M. / Nurizzo, D. / Mason, A.B. / Baker, E.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structures of two mutants that probe the role in iron release of the dilysine pair in the N-lobe of human transferrin.
Authors: Baker, H.M. / Nurizzo, D. / Mason, A.B. / Baker, E.N.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Serotransferrin
A: Serotransferrin
C: Serotransferrin
D: Serotransferrin
E: Serotransferrin
F: Serotransferrin
G: Serotransferrin
H: Serotransferrin
I: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,97927
Polymers334,9369
Non-polymers1,04318
Water1,29772
1
B: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,2151
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.462, 97.897, 208.953
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B C
12D E F G H I

NCS domain segments:

Dom-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: CO3 / End label comp-ID: CO3 / Refine code: 1 / Auth seq-ID: 3 - 600 / Label seq-ID: 3

Component-IDEns-IDAuth asym-IDLabel asym-ID
11AB - M
21BA - K
31CC - O
12DD - Q
22EE - S
32FF - U
42GG - W
52HH - Y
62II - AA

NCS ensembles :
ID
1
2

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Components

#1: Protein
Serotransferrin / Transferrin / Siderophilin / Beta-1-metal-binding globulin


Mass: 37215.137 Da / Num. of mol.: 9 / Fragment: N-lobe / Mutation: K206E, K296E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNUT / Cell line (production host): BHK / Organ (production host): kidney / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P02787
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Protein: 35mg/ml, 0.1M ammonium bicarbonate. Well: 20% PEG 3350, 0.2 M potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 2006 / Details: Osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→48 Å / Num. all: 83306 / Num. obs: 83306 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.2 / % possible all: 98.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å47.64 Å
Translation2.8 Å47.64 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild type transferrin. PDB entry code 1A8E.

1a8e


Resolution: 2.8→29.76 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.893 / SU B: 41.761 / SU ML: 0.373 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25885 4132 5 %RANDOM
Rwork0.22961 ---
obs0.23109 78012 97.33 %-
all-82144 --
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: 57.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.2 Å2
2---0.28 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22950 0 45 72 23067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02223607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9631977
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99352952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1624.51080
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55153897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.61215108
X-RAY DIFFRACTIONr_chiral_restr0.0930.23375
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.210736
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.216095
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2751
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.219
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3170.2130
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.441.515124
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.854223580
X-RAY DIFFRACTIONr_scbond_it1.29939615
X-RAY DIFFRACTIONr_scangle_it2.3134.58397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 2556 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
1Btight positional0.020
1Ctight positional0.020
2Dtight positional0.040.05
2Etight positional0.040
2Ftight positional0.040
2Gtight positional0.030
2Htight positional0.030
2Itight positional0.030
1Atight thermal0.050.5
1Btight thermal0.050
1Ctight thermal0.050
2Dtight thermal0.060.5
2Etight thermal0.060
2Ftight thermal0.060
2Gtight thermal0.060
2Htight thermal0.060
2Itight thermal0.050
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 312 -
Rwork0.381 5706 -
obs--96.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.38221.0388-0.61266.73040.93645.91620.03490.02450.00790.0754-0.49270.4979-0.0964-0.33540.4578-0.3979-0.0038-0.0971-0.3165-0.0265-0.3991-64.5832.05549.026
26.1492-1.4667-0.36662.74140.93795.9293-0.32790.2592-0.37590.2029-0.13590.26720.376-0.08970.4638-0.4019-0.00870.0517-0.28350.047-0.4067-47.0861.71690.301
34.72412.28990.93434.4566-0.23596.1158-0.4166-0.17740.4285-0.2484-0.06030.2251-0.245-0.24570.4769-0.3864-0.0051-0.0003-0.3196-0.0912-0.4005-17.50615.73920.646
44.1631.9255-0.2314.2139-1.00276.1668-0.1733-0.10940.35970.0401-0.1456-0.0942-0.85440.14530.3189-0.29-0.0542-0.2055-0.2023-0.0594-0.3673-56.95442.62782.362
52.6387-0.8419-0.97915.85210.34026.2065-0.1488-0.0888-0.24690.1099-0.205-0.29330.60570.70080.3538-0.24180.0310.0285-0.24540.1895-0.4051-61.90152.75912.705
65.94810.82560.77212.3852-0.58396.4894-0.22090.0728-0.1199-0.1386-0.1401-0.3570.2920.8410.3611-0.33-0.03880.1333-0.16080.1324-0.4066-34.1113.06556.947
77.29165.19-2.71446.4943-1.72734.3723-0.52350.6022-0.3114-0.2810.511-0.0930.1764-0.20.0125-0.2345-0.12880.050.1827-0.0792-0.3446-15.00461.48386.849
810.97462.41482.60052.4061.40474.35170.3486-0.72460.22490.0725-0.35330.25380.0383-0.16190.0046-0.0867-0.23380.0280.0237-0.0587-0.3223.18829.99752.465
92.5209-2.3605-0.075411.07873.05814.26990.0926-0.09120.0705-0.907-0.08320.3329-0.2096-0.0189-0.00940.1361-0.0998-0.0927-0.19460.0051-0.3292-66.5796.97717.182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB3 - 3313 - 331
2X-RAY DIFFRACTION2BA3 - 3313 - 331
3X-RAY DIFFRACTION3CC3 - 3313 - 331
4X-RAY DIFFRACTION4DD3 - 3313 - 331
5X-RAY DIFFRACTION5EE3 - 3313 - 331
6X-RAY DIFFRACTION6FF3 - 3313 - 331
7X-RAY DIFFRACTION7GG3 - 3313 - 331
8X-RAY DIFFRACTION8HH3 - 3313 - 331
9X-RAY DIFFRACTION9II3 - 3313 - 331

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