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- PDB-7w7c: Heme exporter in the unliganded form -

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Basic information

Entry
Database: PDB / ID: 7w7c
TitleHeme exporter in the unliganded form
Components
  • Putative ABC transport system integral membrane protein
  • Putative ABC transport system, ATP-binding protein
KeywordsMEMBRANE PROTEIN / Heme efflux / Heme detoxification / heme extraction / 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 / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRahman, M.M. / Hisano, T. / Nakamura, H. / 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 1.1Jan 11, 2023Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)60,8143
Polymers60,7182
Non-polymers961
Water21612
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)121,6276
Polymers121,4354
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7700 Å2
ΔGint-82 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.752, 100.550, 191.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 24851.355 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star / References: UniProt: Q6NEF1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.75 Å3/Da / Density % sol: 74.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 21% PEG 2000, 0.1 M NaCl, 0.2 M NH4 sulfate, 3 mM CHAPS, 5 mM CuCl2, 0.1 M Na citrate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.35 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.35 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 31536 / % possible obs: 91.8 % / Redundancy: 11 % / Biso Wilson estimate: 44.29 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Χ2: 0.868 / Net I/σ(I): 11 / Num. measured all: 345399
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.75.70.21510430.9880.0920.2361.21362.1
2.7-2.746.60.1911010.9820.0710.2040.90765.5
2.74-2.87.40.16711450.9870.0590.1780.85368.3
2.8-2.858.10.14912780.9950.050.1570.8874.7
2.85-2.928.70.17513990.9920.0560.1850.85483.9
2.92-2.989.10.16715300.9910.0530.1760.83189.1
2.98-3.069.50.14815580.9940.0470.1560.83193.5
3.06-3.1410.20.13316630.9970.0420.1390.82496.9
3.14-3.2310.90.12516670.9970.0380.1310.84499
3.23-3.3411.60.10917140.9980.0330.1140.86699.7
3.34-3.4612.30.10816900.9980.0320.1130.986100
3.46-3.612.80.09117010.9980.0260.0950.878100
3.6-3.76130.07117190.9980.0210.0740.981100
3.76-3.9612.90.06917030.9990.020.0721.034100
3.96-4.2112.60.0517260.9990.0140.0520.903100
4.21-4.5311.60.0417230.9990.0120.0420.86100
4.53-4.9911.80.03717490.9990.0110.0390.824100
4.99-5.7111.90.03617430.9990.0110.0380.752100
5.71-7.1913.60.03417850.9990.010.0360.758100
7.19-5012.20.02318990.9970.0070.0240.736100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LLI

6lli
PDB Unreleased entry


Resolution: 2.8→49.621 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 1275 4.79 %
Rwork0.2185 25343 -
obs0.2199 26618 90.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.21 Å2 / Biso mean: 67.2909 Å2 / Biso min: 14.84 Å2
Refinement stepCycle: final / Resolution: 2.8→49.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 5 12 2825
Biso mean--28.64 35.32 -
Num. residues----381
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.91210.1989950.1952192063
2.9121-3.04460.1955930.1839225673
3.0446-3.20510.23621020.1928258084
3.2051-3.40590.24151330.2112292195
3.4059-3.66880.20551430.19743089100
3.6688-4.03780.19011780.19063080100
4.0378-4.62170.22131730.19693080100
4.6217-5.82140.28061770.23233131100
5.8214-49.620.31431810.27423286100
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)
12.5172-0.1944-0.41752.049-0.03930.92670.1-0.12590.2684-0.0675-0.1893-0.36050.03990.07310.04540.1329-0.01290.0470.15330.05860.34518.48313.72791.191
20.64970.04750.67680.2190.46042.9038-0.10350.76410.1483-0.63690.13520.1869-0.1828-0.134-0.17941.54890.03950.25861.16530.11230.399114.3754.42351.573
30.2980.05970.4540.01180.06990.984-0.13560.70820.0108-1.0386-0.0289-0.1140.1944-0.0249-0.38881.1612-0.01940.09540.82710.23430.21538.5029.12653.82
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:222 )A1 - 222
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:37 )B1 - 37
3X-RAY DIFFRACTION3( CHAIN B AND RESID 221:342 )B221 - 342

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