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- PDB-7w79: Heme exporter HrtBA in complex with Mn-AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7w79
TitleHeme exporter HrtBA in complex with Mn-AMPPNP
Components
  • Putative ABC transport system integral membrane protein
  • Putative ABC transport system, ATP-binding protein
KeywordsMEMBRANE PROTEIN / Heme efflux / Heme extraction / Heme detoxification / ABC transporter / 4-Helix TMD
Function / homology
Function and homology information


transmembrane transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease family / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease family / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / ABC transport system integral membrane protein / ABC transport system, ATP-binding protein
Similarity search - Component
Biological speciesCorynebacterium diphtheriae NCTC 13129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsHisano, T. / Nakamura, H. / Rahman, M.M. / Tosha, T. / Shirouzu, M. / Shiro, Y.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K07309 Japan
Japan Society for the Promotion of Science (JSPS)26220807 Japan
Japan Society for the Promotion of Science (JSPS)JP19H00926 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05761 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structural basis for heme detoxification by an ATP-binding cassette-type efflux pump in gram-positive pathogenic bacteria.
Authors: Nakamura, H. / Hisano, T. / Rahman, M.M. / Tosha, T. / Shirouzu, M. / Shiro, Y.
History
DepositionDec 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ABC transport system, ATP-binding protein
B: Putative ABC transport system integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2158
Polymers59,4332
Non-polymers7826
Water00
1
A: Putative ABC transport system, ATP-binding protein
B: Putative ABC transport system integral membrane protein
hetero molecules

A: Putative ABC transport system, ATP-binding protein
B: Putative ABC transport system integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,43016
Polymers118,8664
Non-polymers1,56412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area13890 Å2
ΔGint-100 kcal/mol
Surface area44110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.369, 169.369, 95.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Putative ABC transport system, ATP-binding protein


Mass: 23566.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP2323 / Plasmid: pRSET-C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q6NEF2
#2: Protein Putative ABC transport system integral membrane protein


Mass: 35866.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae NCTC 13129 (bacteria)
Strain: ATCC 700971 / NCTC 13129 / Biotype gravis / Gene: DIP2324 / Plasmid: pRSET-C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q6NEF1
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
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: 5.73 Å3/Da / Density % sol: 78.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 22% PEG 4000, 10 mM Na acetate, 10 mM MnCl2, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.89236 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89236 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 28470 / % possible obs: 99.8 % / Redundancy: 14 % / Biso Wilson estimate: 44.02 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.037 / Rrim(I) all: 0.128 / Χ2: 0.909 / Net I/σ(I): 6.4 / Num. measured all: 399387
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.99-3.049.413860.5440.5050.87799.9
3.04-3.112.113930.7040.420.83999.2
3.1-3.1613.514030.8030.3380.85100
3.16-3.2214.413770.8660.2570.88399.40.9510.986
3.22-3.2914.514050.9210.2040.87899.60.7590.786
3.29-3.3714.613870.9390.1660.8571000.620.642
3.37-3.4514.514070.9650.1280.89499.70.4770.494
3.45-3.5414.514030.980.0980.87399.80.3670.38
3.54-3.6514.614200.9820.0860.8881000.320.331
3.65-3.7714.613960.9870.0681.07999.90.2550.264
3.77-3.914.614060.9940.0530.96399.90.1980.205
3.9-4.0614.614160.9950.0420.911000.1550.16
4.06-4.2414.614290.9960.0330.8981000.1210.125
4.24-4.4714.614210.9970.0270.8871000.1010.105
4.47-4.7514.514260.9970.0250.9131000.0930.097
4.75-5.1114.514370.9970.0271.0381000.10.104
5.11-5.6314.414390.9960.031.171000.1120.116
5.63-6.4414.414540.9960.031.1511000.1120.116
6.44-8.1114.214920.9990.0180.7981000.0640.067
8.11-5013.315730.9990.010.49699.50.0350.037

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→48.54 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2606 1792 7.18 %
Rwork0.2203 23155 -
obs0.2233 24947 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 277.87 Å2 / Biso mean: 90.5491 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3.1→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 48 0 4164
Biso mean--54.66 --
Num. residues----560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094214
X-RAY DIFFRACTIONf_angle_d1.145750
X-RAY DIFFRACTIONf_chiral_restr0.053709
X-RAY DIFFRACTIONf_plane_restr0.007728
X-RAY DIFFRACTIONf_dihedral_angle_d15.4832503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.18390.37591200.3241155786
3.1839-3.27760.30941260.2743167093
3.2776-3.38340.34321330.253171495
3.3834-3.50430.25361330.2534174698
3.5043-3.64450.28131390.2307175797
3.6445-3.81030.30131400.2299177999
3.8103-4.01110.27081360.2182176298
4.0111-4.26230.24671410.20361823100
4.2623-4.59110.24541420.1861824100
4.5911-5.05270.21141430.17711832100
5.0527-5.78290.2291430.19721847100
5.7829-7.28180.21781460.2271883100
7.2818-48.540.24631500.2135196199

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