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- PDB-8tv8: Crystal structure of nontypeable Haemophilus influenzae SapA -

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Basic information

Entry
Database: PDB / ID: 8tv8
TitleCrystal structure of nontypeable Haemophilus influenzae SapA
ComponentsABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
KeywordsPEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle
Similarity search - Domain/homology
ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
Similarity search - Component
Biological speciesHaemophilus influenzae 86-028NP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsTanaka, K.J. / Buechel, E.R. / Rivera, K.G. / Pinkett, H.W.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM140584 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM140584-04S1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI139519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008382 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008449 United States
CitationJournal: Biochemistry / Year: 2024
Title: Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae .
Authors: Rivera, K.G. / Tanaka, K.J. / Buechel, E.R. / Origel Jr., O. / Harrison, A. / Mason, K.M. / Pinkett, H.W.
History
DepositionAug 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance


Theoretical massNumber of molelcules
Total (without water)64,4921
Polymers64,4921
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.755, 119.755, 129.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance


Mass: 64492.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae 86-028NP (bacteria)
Gene: sapA, NTHI1401 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QL73
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.6 Å3/Da / Density % sol: 65.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.4
Details: 0.1 M Tris pH 9.4, 1.5 M ammonium phosphate, 0.18 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.25→44.014 Å / Num. obs: 45307 / % possible obs: 99.9 % / Redundancy: 19.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.021 / Rrim(I) all: 0.091 / Χ2: 0.94 / Net I/σ(I): 16.1
Reflection shellResolution: 2.25→2.32 Å / % possible obs: 100 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.718 / Num. measured all: 81561 / Num. unique obs: 4108 / CC1/2: 0.939 / Rpim(I) all: 0.165 / Rrim(I) all: 0.737 / Χ2: 0.88 / Net I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
ARP/wARPmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→44.014 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.866 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.225 2322 5.133 %
Rwork0.197 42917 -
all0.198 --
obs-45239 99.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.113 Å20 Å20 Å2
2---0.113 Å20 Å2
3---0.227 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 0 114 4266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124253
X-RAY DIFFRACTIONr_bond_other_d0.0120.0163826
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.6485779
X-RAY DIFFRACTIONr_angle_other_deg0.6221.5618923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.333523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63210722
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.68410210
X-RAY DIFFRACTIONr_chiral_restr0.0760.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
X-RAY DIFFRACTIONr_nbd_refined0.2160.2711
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23485
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22039
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22243
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.225
X-RAY DIFFRACTIONr_nbd_other0.1450.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0750.23
X-RAY DIFFRACTIONr_mcbond_it5.3985.4672050
X-RAY DIFFRACTIONr_mcbond_other5.3995.4682050
X-RAY DIFFRACTIONr_mcangle_it7.0578.182559
X-RAY DIFFRACTIONr_mcangle_other7.0568.1812560
X-RAY DIFFRACTIONr_scbond_it6.1016.052203
X-RAY DIFFRACTIONr_scbond_other6.16.0512204
X-RAY DIFFRACTIONr_scangle_it8.6578.8413220
X-RAY DIFFRACTIONr_scangle_other8.6568.8433221
X-RAY DIFFRACTIONr_lrange_it10.77968.3464542
X-RAY DIFFRACTIONr_lrange_other10.77868.3564539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.25-2.3080.3081830.25231090.25532930.9470.96599.96960.22
2.308-2.3710.2871690.23830290.2431980.9480.9681000.206
2.371-2.440.2581660.23129440.23231100.9610.971000.201
2.44-2.5150.3231610.23428620.23930230.940.9691000.206
2.515-2.5970.2811380.22828370.23129750.9570.9711000.203
2.597-2.6880.2971350.23226960.23528310.9480.9691000.212
2.688-2.7890.2911130.24126570.24327700.9540.9651000.226
2.789-2.9020.2631350.22625040.22826390.950.9681000.217
2.902-3.0310.2711150.22324450.22525600.9620.9691000.22
3.031-3.1780.2481270.23323090.23324360.9610.9661000.24
3.178-3.3490.289970.23922440.24123410.9450.9661000.25
3.349-3.5510.2831180.22521050.22822230.9520.9731000.244
3.551-3.7940.2041230.19819570.19920800.9750.9791000.218
3.794-4.0950.191300.1718280.17119580.980.9831000.199
4.095-4.4820.158940.14117150.14118090.9870.9881000.175
4.482-5.0050.16860.13515740.13716600.9840.9891000.169
5.005-5.7670.192790.16113890.16214680.980.9851000.2
5.767-7.0330.234800.18711950.1912750.9650.981000.234
7.033-9.8210.214470.1799580.18110070.9710.9899.80140.24
9.821-44.0140.183260.2425600.2396340.9790.95592.4290.327

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