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- PDB-7ofz: Nontypeable Haemophillus influenzae SapA in complex with double s... -

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Basic information

Entry
Database: PDB / ID: 7ofz
TitleNontypeable Haemophillus influenzae SapA in complex with double stranded RNA
Components
  • ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
  • RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
KeywordsPEPTIDE BINDING PROTEIN / NTHi / RNA binding / peptide binding / substrate binding protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / metal ion binding
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
RNA / RNA (> 10) / ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å
AuthorsLukacik, P. / Owen, C.D. / Nettleship, J.E. / Bird, L.E. / Owens, R.J. / Walsh, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M010937/1 United Kingdom
CitationJournal: Plos One / Year: 2021
Title: The structure of nontypeable Haemophilus influenzae SapA in a closed conformation reveals a constricted ligand-binding cavity and a novel RNA binding motif.
Authors: Lukacik, P. / Owen, C.D. / Harris, G. / Bolla, J.R. / Picaud, S. / Alibay, I. / Nettleship, J.E. / Bird, L.E. / Owens, R.J. / Biggin, P.C. / Filippakopoulos, P. / Robinson, C.V. / Walsh, M.A.
History
DepositionMay 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2403
Polymers66,2172
Non-polymers231
Water2,054114
1
A: ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
C: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
hetero molecules

C: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)72,3534
Polymers72,3303
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-15 kcal/mol
Surface area24190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.400, 144.400, 62.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

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


Mass: 60102.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain 86-028NP) (bacteria)
Strain: 86-028NP / Gene: sapA, NTHI1401 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QL73
#2: RNA chain RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')


Mass: 6113.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: This RNA sequence is the best interpretation of the electron density
Source: (natural) Escherichia coli (E. coli)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% (w/v) PEG 3350, 0.25 M NaBr, 0.1 M Bis-Tris Propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.62→72.2 Å / Num. obs: 19346 / % possible obs: 95.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 89.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.129 / Χ2: 0.966 / Net I/σ(I): 13.08 / Num. measured all: 145122 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.62-2.694.0261.5710.7427000.3551.80497.1
2.69-2.764.0831.2820.9826250.411.47196.6
2.76-2.843.9321.0181.324850.5961.17493.4
2.84-2.933.8830.8941.5922060.641.03586.5
2.93-3.033.9850.6572.3822950.7840.7692.1
3.03-3.134.040.4494.0323730.8980.51798.2
3.13-3.254.0040.3315.6722770.9360.38198.8
3.25-3.384.0750.2867.1921920.9510.3398.4
3.38-3.534.0730.210.3721070.9770.23197.9
3.53-3.714.1160.15313.2419680.9880.17696.5
3.71-3.914.1290.11217.518700.9910.12895.4
3.91-4.144.0190.08420.8217230.9950.09792.8
4.14-4.434.0080.06524.6314590.9960.07584.1
4.43-4.784.1710.05129.6915860.9970.05898.5
4.78-5.244.2080.04731.2514610.9980.05498.3
5.24-5.864.1790.04431.3712750.9980.0596.7
5.86-6.774.1830.04232.0111430.9980.04995.7
6.77-8.294.0840.03238.28820.9980.03787.9
8.29-11.724.2330.02549.017050.9990.02992
11.72-72.24.1230.02352.743210.02797.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.13 Å102.11 Å
Translation7.13 Å102.11 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.5.6phasing
BALBESphasing
BUSTER2.10.3refinement
REFMAC7.04.09refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
PHENIXmodel building
PHENIX2.5.6refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M8U

3m8u


Resolution: 2.62→72.2 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.892 / SU R Cruickshank DPI: 1.138 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.033 / SU Rfree Blow DPI: 0.34 / SU Rfree Cruickshank DPI: 0.339
RfactorNum. reflection% reflectionSelection details
Rfree0.263 940 4.88 %RANDOM
Rwork0.217 ---
obs0.219 19270 94.9 %-
Displacement parametersBiso max: 175.85 Å2 / Biso mean: 69.57 Å2 / Biso min: 32.96 Å2
Baniso -1Baniso -2Baniso -3
1-9.6377 Å20 Å20 Å2
2--9.6377 Å20 Å2
3----19.2754 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.62→72.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 407 1 114 4518
Biso mean--66.27 54.09 -
Num. residues----516
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1495SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes713HARMONIC5
X-RAY DIFFRACTIONt_it4559HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion618SEMIHARMONIC5
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_contact5070SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4559HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6286HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion20.12
LS refinement shellResolution: 2.62→2.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 47
RfactorNum. reflection% reflection
Rfree0.3756 18 4.39 %
Rwork0.2696 392 -
all0.2744 410 -
obs--98.77 %

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