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- PDB-7kyo: PsaBC from Streptococcus pneumoniae in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 7kyo
TitlePsaBC from Streptococcus pneumoniae in complex with Fab
Components
  • Fab heavy chain
  • Fab light chain
  • Manganese ABC transporter, ATP-binding protein
  • Manganese ABC transporter, permease protein
KeywordsTRANSPORT PROTEIN/IMMUNE SYSTEM / ABC transporter manganese / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


response to zinc ion / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding
Similarity search - Function
ABC transporter, TroCD-like / ABC 3 transport family / : / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, BtuC-like / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...ABC transporter, TroCD-like / ABC 3 transport family / : / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, BtuC-like / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Manganese ABC transporter, ATP-binding protein / Manganese ABC transporter, permease protein, putative
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 2
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMaher, M.J. / Sjohamn, J.
Funding support Australia, Japan, 7items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1080784 Australia
National Health and Medical Research Council (NHMRC, Australia)1140554 Australia
National Health and Medical Research Council (NHMRC, Australia)1122582 Australia
Australian Research Council (ARC)DP170102102 Australia
Australian Research Council (ARC)FT170100006 Australia
Australian Research Council (ARC)FT180100397 Australia
Japan Agency for Medical Research and Development (AMED)JP20am0101079 Japan
CitationJournal: Sci Adv / Year: 2021
Title: The structural basis of bacterial manganese import.
Authors: Neville, S.L. / Sjohamn, J. / Watts, J.A. / MacDermott-Opeskin, H. / Fairweather, S.J. / Ganio, K. / Carey Hulyer, A. / McGrath, A.P. / Hayes, A.J. / Malcolm, T.R. / Davies, M.R. / Nomura, N. ...Authors: Neville, S.L. / Sjohamn, J. / Watts, J.A. / MacDermott-Opeskin, H. / Fairweather, S.J. / Ganio, K. / Carey Hulyer, A. / McGrath, A.P. / Hayes, A.J. / Malcolm, T.R. / Davies, M.R. / Nomura, N. / Iwata, S. / O'Mara, M.L. / Maher, M.J. / McDevitt, C.A.
History
DepositionDec 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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
B: Manganese ABC transporter, ATP-binding protein
H: Fab heavy chain
L: Fab light chain
C: Manganese ABC transporter, permease protein


Theoretical massNumber of molelcules
Total (without water)106,0004
Polymers106,0004
Non-polymers00
Water59433
1
B: Manganese ABC transporter, ATP-binding protein
H: Fab heavy chain
L: Fab light chain
C: Manganese ABC transporter, permease protein

B: Manganese ABC transporter, ATP-binding protein
H: Fab heavy chain
L: Fab light chain
C: Manganese ABC transporter, permease protein


Theoretical massNumber of molelcules
Total (without water)212,0008
Polymers212,0008
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area22380 Å2
ΔGint-159 kcal/mol
Surface area72330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.660, 241.700, 98.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Manganese ABC transporter, ATP-binding protein / PsaB


Mass: 26879.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: psaB, SPD_1461 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZNF3
#2: Antibody Fab heavy chain


Mass: 25026.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody Fab light chain


Mass: 23949.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Protein Manganese ABC transporter, permease protein / PsaC


Mass: 30145.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: psaC, SPD_1462 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZPI2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris-HCl, pH 8.5, 28% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 34896 / % possible obs: 98.2 % / Redundancy: 4.2 % / CC1/2: 0.999 / Net I/σ(I): 14.6
Reflection shellResolution: 2.85→2.99 Å / Num. unique obs: 4212 / CC1/2: 0.691

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NQ2

2nq2


Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.881 / SU B: 38.2 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R: 1.215 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27056 1689 5.2 %RANDOM
Rwork0.23769 ---
obs0.23936 30603 90.6 %-
Displacement parametersBiso mean: 38.313 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å20 Å2
2--1.47 Å20 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7000 0 0 33 7033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197169
X-RAY DIFFRACTIONr_bond_other_d0.0010.026835
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.9599753
X-RAY DIFFRACTIONr_angle_other_deg0.837315730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.435922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17124.275262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.447151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.31522
X-RAY DIFFRACTIONr_chiral_restr0.0580.21155
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028019
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021583
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3813.9083697
X-RAY DIFFRACTIONr_mcbond_other0.3813.9073696
X-RAY DIFFRACTIONr_mcangle_it0.7095.864613
X-RAY DIFFRACTIONr_mcangle_other0.7095.8614614
X-RAY DIFFRACTIONr_scbond_it0.2443.8763470
X-RAY DIFFRACTIONr_scbond_other0.2443.8753468
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4715.8185138
X-RAY DIFFRACTIONr_long_range_B_refined1.73730.7487650
X-RAY DIFFRACTIONr_long_range_B_other1.73730.7527651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 45 -
Rwork0.33 870 -
obs--35.42 %

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