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- PDB-6xr0: Crystal Structure of Human Melanotransferrin in complex with SC57... -

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Basic information

Entry
Database: PDB / ID: 6xr0
TitleCrystal Structure of Human Melanotransferrin in complex with SC57.32 Fab
Components
  • Melanotransferrin
  • SC57.32 Fab Heavy Chain
  • SC57.32 Fab Light Chain
KeywordsMETAL TRANSPORT / Iron-binding / Ab Complex
Function / homology
Function and homology information


: / protein metabolic process => GO:0019538 / positive regulation of extracellular matrix disassembly / negative regulation of substrate adhesion-dependent cell spreading / : / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of plasminogen activation / post-translational protein modification / Post-translational protein phosphorylation / recycling endosome ...: / protein metabolic process => GO:0019538 / positive regulation of extracellular matrix disassembly / negative regulation of substrate adhesion-dependent cell spreading / : / Post-translational modification: synthesis of GPI-anchored proteins / positive regulation of plasminogen activation / post-translational protein modification / Post-translational protein phosphorylation / recycling endosome / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / iron ion transport / early endosome / iron ion binding / endoplasmic reticulum lumen / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Melanotransferrin / 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
Similarity search - Domain/homology
BICARBONATE ION / : / Melanotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.064 Å
AuthorsHayashi, K. / Longenecker, K.L. / Vivona, S.
CitationJournal: Sci Rep / Year: 2021
Title: Complex of human Melanotransferrin and SC57.32 Fab fragment reveals novel interdomain arrangement with ferric N-lobe and open C-lobe.
Authors: Hayashi, K. / Longenecker, K.L. / Liu, L.Y. / Faust, B. / Prashar, A. / Hampl, J. / Stoll, V. / Vivona, S.
History
DepositionJul 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: SC57.32 Fab Heavy Chain
L: SC57.32 Fab Light Chain
M: Melanotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,04610
Polymers127,8123
Non-polymers1,2347
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-34 kcal/mol
Surface area46980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.829, 136.910, 111.135
Angle α, β, γ (deg.)90.000, 91.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules M

#3: Protein Melanotransferrin / / Melanoma-associated antigen p97


Mass: 80302.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MELTF, MAP97, MFI2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08582

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Antibody , 2 types, 2 molecules HL

#1: Antibody SC57.32 Fab Heavy Chain


Mass: 23844.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody SC57.32 Fab Light Chain


Mass: 23664.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 2 types, 3 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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 / N-Acetylglucosamine


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

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Non-polymers , 5 types, 54 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM sodium acetate, pH 4.6 and 30% PEG300

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.06→111.1 Å / Num. obs: 32506 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rpim(I) all: 0.084 / Net I/σ(I): 12.4
Reflection shellResolution: 3.064→3.117 Å / Num. unique obs: 1623 / Rpim(I) all: 0.621

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.11.7 (19-MAR-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B1X

1b1x


Resolution: 3.064→111.1 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.342
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1728 5.32 %RANDOM
Rwork0.2021 ---
obs0.2033 32506 99.8 %-
Displacement parametersBiso max: 130.9 Å2 / Biso mean: 71.47 Å2 / Biso min: 28.17 Å2
Baniso -1Baniso -2Baniso -3
1-17.663 Å20 Å2-12.3373 Å2
2---18.7958 Å20 Å2
3---1.1327 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 3.064→111.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8545 0 77 50 8672
Biso mean--67.2 48.88 -
Num. residues----1112
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3005SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1523HARMONIC5
X-RAY DIFFRACTIONt_it8873HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1157SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6947SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8873HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg12074HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion20.63
LS refinement shellResolution: 3.064→3.08 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2982 23 3.53 %
Rwork0.296 628 -
obs--99.08 %

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