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- PDB-7og0: Nontypeable Haemophillus influenzae SapA in open and closed confo... -

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Basic information

Entry
Database: PDB / ID: 7og0
TitleNontypeable Haemophillus influenzae SapA in open and closed conformations, 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


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
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: 2.61 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 1.1Nov 10, 2021Group: Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list / Item: _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Jan 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 / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
B: ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
D: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
E: 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)131,4416
Polymers131,3614
Non-polymers802
Water2,828157
1
A: ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
E: 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

D: 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)71,1844
Polymers71,1443
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_374-x-2,-y+2,z-11
2
B: ABC-type transport system, periplasmic component, involved in antimicrobial peptide resistance
D: 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

E: 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)71,1844
Polymers71,1443
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_376-x-2,-y+2,z+11
Unit cell
Length a, b, c (Å)143.260, 147.970, 59.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12D
22E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPHEPHEAA35 - 5592 - 526
21GLYGLYPHEPHEBB35 - 5592 - 526
12CCGGDC2 - 181 - 17
22CCGGED2 - 181 - 17

NCS ensembles :
ID
1
2

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Components

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


Mass: 60217.090 Da / Num. of mol.: 2
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: 5463.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion
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: 2.61→65.74 Å / Num. obs: 38239 / % possible obs: 97.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 52.506 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.102 / Χ2: 0.979 / Net I/σ(I): 8.27 / Num. measured all: 144976 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.61-2.682.0680.5881.510960550153000.5630.76496.3
2.68-2.752.0640.4641.8510609538951390.6850.60395.4
2.75-2.832.0210.3762.2510129525650120.770.48995.4
2.83-2.921.9420.3012.719166498747190.8360.39394.6
2.92-3.011.920.2373.328788499045760.8790.31191.7
3.01-3.122.1390.2014.299666472545180.9250.26195.6
3.12-3.242.1630.1695.279358454143270.9430.21995.3
3.24-3.372.1370.1316.458991442742070.9640.1795
3.37-3.522.1480.1057.988587426239980.9740.13793.8
3.52-3.692.1160.0839.658051403738040.9840.10894.2
3.69-3.892.0980.0711.137619384236310.9890.09194.5
3.89-4.132.0090.05912.776784360933770.9910.07693.6
4.13-4.411.8650.0513.925671341430410.9930.06589.1
4.41-4.772.1630.04516.636509320730090.9950.05993.8
4.77-5.222.1750.04516.445886290227060.9940.05993.2
5.22-5.842.1650.04616.185404266224960.9940.0693.8
5.84-6.742.1460.04815.854592234421400.9940.06391.3
6.74-8.252.0120.03618.673596197117870.9960.04790.7
8.25-11.672.1280.02724.572917151813710.9980.03690.3
11.67-65.742.1960.02628.4616938467710.9970.03591.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.62 Å65.74 Å
Translation7.62 Å65.74 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
xia2data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
Cootmodel building
PHENIXmodel building
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M8U

3m8u


Resolution: 2.61→65.74 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 25.301 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.022 / ESU R Free: 0.331
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1870 4.9 %RANDOM
Rwork0.1965 ---
obs0.1991 36274 96.87 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 253.71 Å2 / Biso mean: 57.766 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.61 Å20 Å2
3---0.63 Å2
Refinement stepCycle: final / Resolution: 2.61→65.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8009 728 2 157 8896
Biso mean--55.14 35.93 -
Num. residues----1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0149037
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177646
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.6112439
X-RAY DIFFRACTIONr_angle_other_deg0.8541.69417929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98523.16443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.322151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8621541
X-RAY DIFFRACTIONr_chiral_restr0.0620.21219
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021774
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A150320.13
12B150320.13
21D16390.06
22E16390.06
LS refinement shellResolution: 2.61→2.678 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 132 -
Rwork0.306 2698 -
all-2830 -
obs--99.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.41440.06470.12530.61990.31850.62240.0646-0.07730.16130.0001-0.0461-0.0676-0.06680.0458-0.01840.0954-0.00440.02090.2317-0.0320.0706-106.502155.58775.622
20.45850.1999-0.23331.4085-0.38840.9816-0.09340.06030.0101-0.00710.066-0.0818-0.0260.10240.02750.05740.0220.00770.2413-0.05520.1014-136.228185.568104.3
35.55033.10090.53876.78380.93916.12110.3101-0.23640.1696-0.05320.12440.53720.0172-1.4308-0.43460.26630.0290.09890.64320.10360.2701-169.356172.998117.731
47.86153.8245-0.08187.3047-2.00915.83560.2267-0.1478-0.4264-0.13530.2375-0.12661.47560.1131-0.46430.53470.0538-0.13690.2427-0.03770.1964-118.145121.84562.86
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 560
2X-RAY DIFFRACTION2B34 - 560
3X-RAY DIFFRACTION3D2 - 18
4X-RAY DIFFRACTION4E2 - 18

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