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- PDB-5hdq: MntC co-structure with mAB 305-78-7 -

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Basic information

Entry
Database: PDB / ID: 5hdq
TitleMntC co-structure with mAB 305-78-7
Components
  • ABC transporter substrate-binding protein
  • Fab Heavy Chain
  • Fab Light Chain
KeywordsTransport protein/Immune System / Transport protein / Monoclonal Antibody / Transport protein-Immune System complex
Function / homology
Function and homology information


metal ion transport / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Sandwich ...Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / ABC superfamily ATP binding cassette transporter, binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsParris, K. / Mosyak, L.
CitationJournal: Plos Pathog. / Year: 2016
Title: High Resolution Mapping of Bactericidal Monoclonal Antibody Binding Epitopes on Staphylococcus aureus Antigen MntC.
Authors: Gribenko, A.V. / Parris, K. / Mosyak, L. / Li, S. / Handke, L. / Hawkins, J.C. / Severina, E. / Matsuka, Y.V. / Anderson, A.S.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
H: Fab Heavy Chain
L: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3745
Polymers81,2263
Non-polymers1482
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-28 kcal/mol
Surface area29400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.712, 41.733, 108.404
Angle α, β, γ (deg.)90.000, 97.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ABC transporter substrate-binding protein / Manganese ABC transporter substrate-binding protein / Mn2+/Zn2+ ABC transporter periplasmic protein


Mass: 33021.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: psaA
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: W8TNQ9

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab Heavy Chain


Mass: 23781.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab Light Chain


Mass: 24422.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 199 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein complex (10 mM HEPES pH 7.5 and 150 mM NaCl) was concentrated to 5.16 mg/mL and crystals grown by the hanging drop method using 1 M LiCl, 0.1 M MES, pH 6.0 and 20% PEG 6K as the precipitating reagents.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→36.6 Å / Num. obs: 43860 / % possible obs: 61.6 % / Redundancy: 1 % / Net I/σ(I): 1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNTBUSTER 2.9.7refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGC

1qgc


Resolution: 1.83→36.6 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.9188 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.224 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.181 / Details: The data completeness is 91% 2.2A
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 2236 5.1 %RANDOM
Rwork0.2071 ---
obs0.2086 43860 61.6 %-
Displacement parametersBiso max: 122.2 Å2 / Biso mean: 43.86 Å2 / Biso min: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1--3.891 Å20 Å2-6.173 Å2
2--2.8902 Å20 Å2
3---1.0008 Å2
Refine analyzeLuzzati coordinate error obs: 0.285 Å
Refinement stepCycle: final / Resolution: 1.83→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5392 0 7 197 5596
Biso mean--48.24 38.02 -
Num. residues----704
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1831SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes795HARMONIC5
X-RAY DIFFRACTIONt_it5525HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion747SEMIHARMONIC5
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_contact6183SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5525HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7511HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion20.2
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2392 4 4.82 %
Rwork0.3956 79 -
all0.3896 83 -
obs--61.6 %

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