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- PDB-9hbl: SmsC2B2 complex from M. jannaschii (monoclinic form) -

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Basic information

Entry
Database: PDB / ID: 9hbl
TitleSmsC2B2 complex from M. jannaschii (monoclinic form)
Components
  • Iron-sulfur cluster assembly SufBD family protein MJ0034
  • Uncharacterized ABC transporter ATP-binding protein MJ0035
KeywordsMETAL TRANSPORT / Iron-sulfur cluster / biogenesis / SMS / Archaea
Function / homology
Function and homology information


iron-sulfur cluster assembly / ATP hydrolysis activity / ATP binding
Similarity search - Function
SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / : / SUF system FeS cluster assembly, SufBD core domain / FeS cluster assembly SUF system, ATPase SufC / 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. ...SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / : / SUF system FeS cluster assembly, SufBD core domain / FeS cluster assembly SUF system, ATPase SufC / 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
Iron-sulfur cluster assembly SufBD family protein MJ0034 / Uncharacterized ABC transporter ATP-binding protein MJ0035
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 Å
AuthorsMechaly, A.E. / Dussouchaud, M. / Haouz, A. / Betton, J.M. / Barras, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: SmsC2B2 complex from M. jannaschii (monoclinic form)
Authors: Mechaly, A.E. / Dussouchaud, M. / Haouz, A. / Betton, J.M. / Barras, F.
History
DepositionNov 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized ABC transporter ATP-binding protein MJ0035
B: Iron-sulfur cluster assembly SufBD family protein MJ0034
C: Uncharacterized ABC transporter ATP-binding protein MJ0035
D: Iron-sulfur cluster assembly SufBD family protein MJ0034
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,54618
Polymers128,5754
Non-polymers97114
Water7,909439
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.291, 132.733, 75.34
Angle α, β, γ (deg.)90, 111.66, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized ABC transporter ATP-binding protein MJ0035 / SmsC


Mass: 28636.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0035 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60350
#2: Protein Iron-sulfur cluster assembly SufBD family protein MJ0034


Mass: 35651.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60349
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1M Ammonium sulfate 0.3M Sodium formate 0.1M Sodium acetate 3% w/v PGA (Na+ form, LM) 3% w/v PEG20000 pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.191→61.931 Å / Num. obs: 42393 / % possible obs: 93.8 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.044 / Rrim(I) all: 0.121 / Net I/σ(I): 8.9
Reflection shellResolution: 2.191→2.46 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2120 / CC1/2: 0.77 / Rpim(I) all: 0.35 / Rrim(I) all: 0.928 / % possible all: 70.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.191→42.3 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.601 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.603 / SU Rfree Blow DPI: 0.296 / SU Rfree Cruickshank DPI: 0.301
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 2104 -RANDOM
Rwork0.2082 ---
obs0.2105 42388 60.1 %-
Displacement parametersBiso mean: 63.15 Å2
Baniso -1Baniso -2Baniso -3
1--5.0214 Å20 Å25.2215 Å2
2--5.058 Å20 Å2
3----0.0366 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.191→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8304 0 59 439 8802
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9911354HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3191SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1416HARMONIC5
X-RAY DIFFRACTIONt_it8481HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1155SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6718SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion18.62
LS refinement shellResolution: 2.191→2.35 Å
RfactorNum. reflection% reflection
Rfree0.2779 27 -
Rwork0.2648 --
obs--6.19 %
Refinement TLS params.

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)
13.24520.6058-0.74910.8939-1.30471.72690.08790.3439-0.20150.34390.3777-0.243-0.2015-0.243-0.4656-0.17460.08930.0208-0.03370.11990.0043-42.261742.5071-11.6082
21.3635-0.2694-0.383800.26120.83970.1047-0.0102-0.0045-0.01020.08270.118-0.00450.118-0.1874-0.1973-0.1050.02380.0004-0.04440.1952-1.026650.4018-14.5349
30.6786-0.5091-0.78281.5944-0.64972.111-0.12990.1909-0.25530.19090.2785-0.0602-0.2553-0.0602-0.14870.03210.11910.1051-0.05070.1118-0.1325-27.759322.66439.8628
41.14950.3613-0.73510-0.11320.9585-0.39590.00230.33010.00230.1153-0.03530.3301-0.03530.28060.0999-0.0540.14590.0399-0.1267-0.1037-9.917414.424-27.6232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-2 - 239
2X-RAY DIFFRACTION2{ B|* }B28 - 316
3X-RAY DIFFRACTION3{ C|* }C-2 - 239
4X-RAY DIFFRACTION4{ D|* }D28 - 316

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