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- PDB-7w78: Heme exporter HrtBA in complex with Mg-AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7w78
TitleHeme exporter HrtBA in complex with Mg-AMPPNP
Components(Putative ABC transport ...) x 2
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 / 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 ...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
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DODECANE / Myristoleic acid / 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: 2.884 Å
AuthorsHisano, T. / Nakamura, H. / Rahman, M.M. / Tosha, T. / Shirouzu, M. / Shiro, Y.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)26220807 Japan
Japan Society for the Promotion of Science (JSPS)16K07309 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

Downloads & links

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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)60,79710
Polymers59,4332
Non-polymers1,3648
Water2,090116
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)121,59420
Polymers118,8664
Non-polymers2,72716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area16010 Å2
ΔGint-85 kcal/mol
Surface area43940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.981, 168.981, 94.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

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Components

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Putative ABC transport ... , 2 types, 2 molecules AB

#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

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Non-polymers , 7 types, 124 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MYZ / Myristoleic acid / Z-tetradec-9-enoic acid


Mass: 226.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26O2
#8: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.69 Å3/Da / Density % sol: 78.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 400, 10 mM Mg acetate, 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 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 31561 / % possible obs: 100 % / Redundancy: 28.4 % / Biso Wilson estimate: 40.15 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.029 / Rrim(I) all: 0.115 / Χ2: 0.971 / Net I/σ(I): 5.5 / Num. measured all: 897604
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.88-2.9318.315400.4830.5660.80999.9
2.93-2.9823.415460.6070.5210.815100
2.98-3.0426.915410.7630.3980.858100
3.04-3.128.815450.8130.3190.889100
3.1-3.1729.815720.8720.250.904100
3.17-3.2429.815540.9330.1930.976100
3.24-3.323015310.9460.160.9621000.8630.878
3.32-3.4129.915640.9680.1230.9561000.6650.677
3.41-3.5129.815700.9810.09411000.5050.513
3.51-3.6329.915610.9860.0720.961000.3910.397
3.63-3.7629.915540.9920.0550.9941000.2950.3
3.76-3.9129.815720.9960.0420.9961000.2270.231
3.91-4.0929.815660.9970.0310.9451000.1660.169
4.09-4.329.615880.9980.0230.9211000.1260.128
4.3-4.5729.715660.9990.0180.8931000.0960.098
4.57-4.9229.615960.9990.0160.941000.0880.09
4.92-5.4229.315940.9990.0191.1741000.1040.106
5.42-6.22916160.9980.0221.5131000.1180.12
6.2-7.8128.616400.9990.0141.2791000.0740.075
7.81-5026.7174510.0040.50799.50.0220.023

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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: MOLECULAR REPLACEMENT
Starting model: 6LLP

6llp
PDB Unreleased entry


Resolution: 2.884→48.406 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 1908 6.92 %
Rwork0.2211 25667 -
obs0.2232 27575 87.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.02 Å2 / Biso mean: 42.6349 Å2 / Biso min: 18.35 Å2
Refinement stepCycle: final / Resolution: 2.884→48.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4160 0 86 116 4362
Biso mean--40.82 35.41 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084311
X-RAY DIFFRACTIONf_angle_d0.8965869
X-RAY DIFFRACTIONf_chiral_restr0.047718
X-RAY DIFFRACTIONf_plane_restr0.005741
X-RAY DIFFRACTIONf_dihedral_angle_d15.6052558
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.884-2.95580.4479380.324950425
2.9558-3.03570.3358860.3357110054
3.0357-3.12510.35721240.2893170483
3.1251-3.22590.28261390.2657182089
3.2259-3.34120.25321420.2451192193
3.3412-3.47490.27951470.2367194094
3.4749-3.6330.28891500.228197095
3.633-3.82450.22861430.2143199497
3.8245-4.0640.21581520.2076205698
4.064-4.37760.22351510.1943207299
4.3776-4.81770.2181550.1882094100
4.8177-5.5140.23381570.20522110100
5.514-6.94380.27041580.21682140100
6.9438-48.40.23191660.2104224299
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)
10.83880.108-0.4650.49340.23731.1285-0.02340.2776-0.1125-0.3345-0.06120.00060.0444-0.2198-0.03120.52240.22340.01760.2651-0.11930.04366.229695.298426.9912
21.05680.2712-0.42270.1266-0.35251.2033-0.21680.4745-0.4076-0.54950.06510.19920.4445-0.3510.19830.5007-0.0056-0.10940.3584-0.23280.27652.070791.209529.5327
31.8146-1.03880.57650.85990.46542.5784-0.0136-0.2529-0.7445-0.1417-0.04120.48780.5655-0.3384-0.10850.30570.0913-0.01050.13860.00960.368650.873391.988849.245
40.9709-0.56-0.25761.0428-0.0670.7872-0.0946-0.0884-0.2694-0.0531-0.02180.17970.109-0.0560.02650.16590.23290.01570.1504-0.00190.156960.364891.962749.6197
50.4675-0.3231-0.24430.95320.27830.24960.01770.0436-0.217-0.0441-0.1345-0.06170.24690.0641-0.40610.49170.19970.01860.17770.05410.333865.965980.781946.534
61.14690.3124-0.13361.2853-0.24180.0987-0.050.3083-0.4561-0.3046-0.1246-0.29060.26390.0818-0.10380.40010.23820.07030.2346-0.06280.297772.274286.505734.5934
70.4282-0.1915-0.09510.50230.03980.16120.09560.0845-0.26620.03580.05820.3348-0.0921-0.10960.1770.46240.49830.09240.43120.10420.286234.8021121.591652.0646
81.0242-0.4005-0.30750.15570.1210.09110.13210.5479-0.5202-1.02270.07740.41690.4674-0.15670.07211.03560.0546-0.29220.3015-0.08270.4797-5.6489143.580237.3416
90.40850.2087-0.18220.2011-0.23060.2822-0.13090.1912-0.3789-0.5707-0.19690.1843-0.0052-0.0810.00320.89810.3293-0.04330.3581-0.09870.55975.5691140.767336.682
100.3227-0.44460.02751.0246-0.01830.25350.09270.0078-0.2948-0.04880.09920.359-0.2562-0.33060.20010.23940.50440.07520.45670.04280.3835.7919120.221444.0909
112.0574-0.83621.11380.436-0.82742.07830.41250.4047-0.2425-0.9784-0.06720.55560.5934-0.2427-0.17950.74080.1272-0.24810.26920.0650.4374-1.2599144.184338.8328
121.94670.14010.12991.61550.11631.46670.2287-0.3513-0.12150.2206-0.04870.1680.34740.0319-0.11950.22530.06350.08490.08320.12150.26282.4027152.1156.3375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 65 )A3 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 88 )A66 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 126 )A89 - 126
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 171 )A127 - 171
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 188 )A172 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 220 )A189 - 220
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 42 )B1 - 42
8X-RAY DIFFRACTION8chain 'B' and (resid 179 through 200 )B179 - 200
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 213 )B201 - 213
10X-RAY DIFFRACTION10chain 'B' and (resid 214 through 344 )B214 - 344
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 82 )B43 - 82
12X-RAY DIFFRACTION12chain 'B' and (resid 83 through 178 )B83 - 178

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