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- PDB-3h0t: Hepcidin-Fab complex -

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Basic information

Entry
Database: PDB / ID: 3h0t
TitleHepcidin-Fab complex
Components
  • Fab fragment, Heavy chain
  • Fab fragment, Light chain
  • Hepcidin
KeywordsIMMUNE SYSTEM/Antimicrobial Protein / Peptide-Fab complex / Antibiotic / Antimicrobial / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Fungicide / Hormone / Secreted / IMMUNE SYSTEM-Antimicrobial Protein COMPLEX
Function / homology
Function and homology information


negative regulation of iron export across plasma membrane / negative regulation of intestinal absorption / negative regulation of iron ion transmembrane transport / response to iron ion / transporter regulator activity / defense response to fungus / hormone activity / multicellular organismal-level iron ion homeostasis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / killing of cells of another organism ...negative regulation of iron export across plasma membrane / negative regulation of intestinal absorption / negative regulation of iron ion transmembrane transport / response to iron ion / transporter regulator activity / defense response to fungus / hormone activity / multicellular organismal-level iron ion homeostasis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / killing of cells of another organism / intracellular iron ion homeostasis / defense response to bacterium / immune response / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Hepcidin / Hepcidin / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSyed, R. / Li, V.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Hepcidin revisited, disulfide connectivity, dynamics, and structure.
Authors: Jordan, J.B. / Poppe, L. / Haniu, M. / Arvedson, T. / Syed, R. / Li, V. / Kohno, H. / Kim, H. / Schnier, P.D. / Harvey, T.S. / Miranda, L.P. / Cheetham, J. / Sasu, B.J.
History
DepositionApr 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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: Fab fragment, Light chain
B: Fab fragment, Heavy chain
C: Hepcidin


Theoretical massNumber of molelcules
Total (without water)51,4363
Polymers51,4363
Non-polymers00
Water6,593366
1
A: Fab fragment, Light chain
B: Fab fragment, Heavy chain
C: Hepcidin

A: Fab fragment, Light chain
B: Fab fragment, Heavy chain
C: Hepcidin


Theoretical massNumber of molelcules
Total (without water)102,8726
Polymers102,8726
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11700 Å2
ΔGint-85 kcal/mol
Surface area38200 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-37 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.077, 52.169, 65.630
Angle α, β, γ (deg.)90.00, 99.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-355-

HOH

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Components

#1: Antibody Fab fragment, Light chain


Mass: 23132.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab fragment, Heavy chain


Mass: 25501.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Hepcidin / Liver-expressed antimicrobial peptide / LEAP-1 / Putative liver tumor regressor / PLTR / Hepcidin- ...Liver-expressed antimicrobial peptide / LEAP-1 / Putative liver tumor regressor / PLTR / Hepcidin-25 / Hepc25 / Hepcidin-20 / Hepc20


Mass: 2802.455 Da / Num. of mol.: 1 / Fragment: UNP residues 60-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAMP, HEPC, hepcidin, LEAP1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P81172
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES,70% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→86.07 Å / Num. obs: 41776 / % possible obs: 94 % / Observed criterion σ(F): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 25.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8FAB

8fab


Resolution: 1.89→86.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.076 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.151 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25085 2225 5.1 %RANDOM
Rwork0.20217 ---
obs0.20464 41776 94.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.371 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å2-0.34 Å2
2--2.69 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.89→86.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 0 366 3821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223548
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2451.9514848
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4615458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89424.453128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72215548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6051512
X-RAY DIFFRACTIONr_chiral_restr0.1650.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022670
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21502
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22403
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2317
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4841.52356
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42223747
X-RAY DIFFRACTIONr_scbond_it3.52931391
X-RAY DIFFRACTIONr_scangle_it5.2684.51101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 127 -
Rwork0.281 2151 -
obs--66.3 %

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