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

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Basic information

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


response to zinc ion / ATP-binding cassette (ABC) transporter complex / cellular response to iron ion / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE / PHOSPHATE ION / Manganese ABC transporter, ATP-binding protein / Manganese import system permease protein ScaB
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Manganese ABC transporter, ATP-binding protein
B: Manganese ABC transporter, permease protein
C: Manganese ABC transporter, ATP-binding protein
D: Manganese ABC transporter, permease protein
E: Manganese ABC transporter, ATP-binding protein
F: Manganese ABC transporter, permease protein
G: Manganese ABC transporter, ATP-binding protein
H: Manganese ABC transporter, permease protein
I: Manganese ABC transporter, ATP-binding protein
J: Manganese ABC transporter, permease protein
K: Manganese ABC transporter, ATP-binding protein
L: Manganese ABC transporter, permease protein
M: Manganese ABC transporter, ATP-binding protein
N: Manganese ABC transporter, permease protein
O: Manganese ABC transporter, ATP-binding protein
P: Manganese ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,50128
Polymers463,70716
Non-polymers2,79412
Water21612
1
A: Manganese ABC transporter, ATP-binding protein
B: Manganese ABC transporter, permease protein
C: Manganese ABC transporter, ATP-binding protein
D: Manganese ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6257
Polymers115,9274
Non-polymers6993
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-115 kcal/mol
Surface area39880 Å2
MethodPISA
2
E: Manganese ABC transporter, ATP-binding protein
F: Manganese ABC transporter, permease protein
G: Manganese ABC transporter, ATP-binding protein
H: Manganese ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6257
Polymers115,9274
Non-polymers6993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-120 kcal/mol
Surface area39900 Å2
MethodPISA
3
I: Manganese ABC transporter, ATP-binding protein
J: Manganese ABC transporter, permease protein
K: Manganese ABC transporter, ATP-binding protein
L: Manganese ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6257
Polymers115,9274
Non-polymers6993
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11450 Å2
ΔGint-115 kcal/mol
Surface area40650 Å2
MethodPISA
4
M: Manganese ABC transporter, ATP-binding protein
N: Manganese ABC transporter, permease protein
O: Manganese ABC transporter, ATP-binding protein
P: Manganese ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6257
Polymers115,9274
Non-polymers6993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-112 kcal/mol
Surface area40130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.550, 129.560, 169.620
Angle α, β, γ (deg.)95.35, 92.21, 98.66
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 26879.217 Da / Num. of mol.: 8
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: Protein
Manganese ABC transporter, permease protein / PsaC


Mass: 31084.178 Da / Num. of mol.: 8
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
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MA4 / CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE


Mass: 508.600 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H44O11
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.37 Å3/Da / Density % sol: 71.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.5, 0.2 M calcium chloride dihydrate, 33% 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: 2.9→50 Å / Num. obs: 156113 / % possible obs: 91.7 % / Redundancy: 4.2 % / Rpim(I) all: 0.08 / Net I/σ(I): 9.4
Reflection shellResolution: 2.9→3 Å / Num. unique obs: 15332 / Rpim(I) all: 0.697

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0218refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7KYO

7kyo


Resolution: 2.9→49.63 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.858 / SU B: 29.142 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 7870 5 %RANDOM
Rwork0.26041 ---
obs0.26145 148164 90.82 %-
Displacement parametersBiso mean: 39.333 Å2
Baniso -1Baniso -2Baniso -3
1-14.11 Å27.55 Å25.61 Å2
2---9.01 Å2-2.1 Å2
3----5.1 Å2
Refinement stepCycle: 1 / Resolution: 2.9→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30985 0 180 12 31177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01931765
X-RAY DIFFRACTIONr_bond_other_d0.0010.0231221
X-RAY DIFFRACTIONr_angle_refined_deg0.7121.97743095
X-RAY DIFFRACTIONr_angle_other_deg0.662372013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.97454077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40424.3051087
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.416155419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1971569
X-RAY DIFFRACTIONr_chiral_restr0.0380.25325
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0234500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026297
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_it0.284.01716326
X-RAY DIFFRACTIONr_mcbond_other0.284.01716325
X-RAY DIFFRACTIONr_mcangle_it0.5346.02320382
X-RAY DIFFRACTIONr_mcangle_other0.5346.02320383
X-RAY DIFFRACTIONr_scbond_it0.1154.08115439
X-RAY DIFFRACTIONr_scbond_other0.1134.07615408
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2576.10322661
X-RAY DIFFRACTIONr_long_range_B_refined2.01549.2935841
X-RAY DIFFRACTIONr_long_range_B_other2.01549.28335839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å
RfactorNum. reflection% reflection
Rfree0.408 509 -
Rwork0.358 9546 -
obs--78.94 %

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