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- PDB-7ofw: Nontypeable Haemophillus influenzae SapA in complex with heme -

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Basic information

Entry
Database: PDB / ID: 7ofw
TitleNontypeable Haemophillus influenzae SapA in complex with heme
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*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')
KeywordsPEPTIDE BINDING PROTEIN / NTHi / RNA binding / peptide binding / substrate binding protein / heme
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
PROTOPORPHYRIN IX CONTAINING FE / 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: 3.15 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

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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
C: RNA (5'-R(P*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)66,5543
Polymers65,9382
Non-polymers6161
Water362
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*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*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)72,3634
Polymers71,7463
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)142.730, 142.730, 60.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-601-

HEM

21A-601-

HEM

31A-702-

HOH

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Components

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


Mass: 60129.066 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*GP*GP*GP*GP*GP*GP*GP*GP*G)-3')


Mass: 5808.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Plasmid details: RNA copurified with the protein
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.43 %
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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.15→71.47 Å / Num. obs: 11352 / % possible obs: 99.9 % / Redundancy: 5.617 % / Biso Wilson estimate: 79.761 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.135 / Χ2: 0.989 / Net I/σ(I): 16.9 / Num. measured all: 116432
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.15-3.235.5990.9792.3815650.7621.08299.9
3.23-3.325.4510.8353.0114820.8390.92599.9
3.32-3.425.7440.6424.1214440.8930.70799.7
3.42-3.525.6250.5165.0314170.9290.5799.7
3.52-3.645.4570.4127.0213470.9420.457100
3.64-3.775.7010.3528.6813330.9460.387100
3.77-3.915.9340.26710.5512600.9740.29399.8
3.91-4.075.8650.20712.4512620.9850.228100
4.07-4.255.5040.15414.3911420.9880.17100
4.25-4.455.8440.1231711440.9920.13699.9
4.45-4.75.7630.09519.6610780.9940.104100
4.7-4.985.3810.08919.99900.9950.09999.9
4.98-5.325.7970.08720.619650.9950.096100
5.32-5.755.6780.08820.128780.9950.097100
5.75-6.35.3780.079208150.9950.088100
6.3-7.045.5790.06523.467370.9960.072100
7.04-8.135.3280.05126.476560.9970.05799.4
8.13-9.965.4560.04131.175460.9980.045100
9.96-14.095.290.0432.494270.9980.044100
14.09-71.474.8920.04232.182410.9980.04799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.15 Å71.36 Å
Translation3.15 Å71.36 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.5.2phasing
REFMAC7.04.09refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
Cootmodel building
BUCCANEERmodel building
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M8U

3m8u


Resolution: 3.15→71.47 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.2699 / WRfactor Rwork: 0.23 / FOM work R set: 0.803 / SU B: 27.514 / SU ML: 0.451 / SU Rfree: 0.5762 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.576 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 553 4.9 %RANDOM
Rwork0.2422 ---
obs0.2441 10777 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 214.22 Å2 / Biso mean: 93.256 Å2 / Biso min: 39.71 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---1 Å20 Å2
3---2 Å2
Refinement stepCycle: final / Resolution: 3.15→71.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 387 43 2 4395
Biso mean--116.03 40.71 -
Num. residues----511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0144542
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173823
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.6246270
X-RAY DIFFRACTIONr_angle_other_deg0.7521.7078949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6675490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84823.209215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10215683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7631519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024819
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02906
LS refinement shellResolution: 3.15→3.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 43 -
Rwork0.356 790 -
all-833 -
obs--99.76 %

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