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- PDB-3d31: ModBC from Methanosarcina acetivorans -

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Basic information

Entry
Database: PDB / ID: 3d31
TitleModBC from Methanosarcina acetivorans
Components
  • Sulfate/molybdate ABC transporter, ATP-binding protein
  • Sulfate/molybdate ABC transporter, permease protein
KeywordsTRANSPORT PROTEIN / ATP-binding / Nucleotide-binding / Transport / Membrane / Transmembrane
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / transmembrane transport / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Transport-associated OB, type 1 / TOBE domain / MetI-like fold / MetI-like / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain ...Transport-associated OB, type 1 / TOBE domain / MetI-like fold / MetI-like / Molybdate/tungstate binding, C-terminal / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Sulfate/molybdate ABC transporter, ATP-binding protein / Sulfate/molybdate ABC transporter, permease protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsGerber, S. / Comellas-Bigler, M. / Locher, K.P.
CitationJournal: Science / Year: 2008
Title: Structural basis of trans-inhibition in a molybdate/tungstate ABC transporter.
Authors: Gerber, S. / Comellas-Bigler, M. / Goetz, B.A. / Locher, K.P.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 17, 2017Group: Data collection
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfate/molybdate ABC transporter, ATP-binding protein
B: Sulfate/molybdate ABC transporter, ATP-binding protein
C: Sulfate/molybdate ABC transporter, permease protein
D: Sulfate/molybdate ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9936
Polymers143,4974
Non-polymers4962
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-128.4 kcal/mol
Surface area52630 Å2
MethodPISA
2
A: Sulfate/molybdate ABC transporter, ATP-binding protein
C: Sulfate/molybdate ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9963
Polymers71,7492
Non-polymers2481
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-13.8 kcal/mol
Surface area31590 Å2
MethodPISA
3
B: Sulfate/molybdate ABC transporter, ATP-binding protein
D: Sulfate/molybdate ABC transporter, permease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9963
Polymers71,7492
Non-polymers2481
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-12.7 kcal/mol
Surface area31640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.840, 139.460, 207.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sulfate/molybdate ABC transporter, ATP-binding protein


Mass: 38907.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TTZ3
#2: Protein Sulfate/molybdate ABC transporter, permease protein


Mass: 32841.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TTZ4
#3: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.68 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8
Details: 18% (w/v) PEG 3350, 200mM magnesium formate, 50mM Tris-HCl pH 8.0, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9537, 0.9789, 1.2143, 1.2147
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97891
31.21431
41.21471
ReflectionResolution: 3→30 Å / Num. all: 54491 / Num. obs: 42405 / % possible obs: 77.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.6 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 14.4
Reflection shellHighest resolution: 3 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXmodel building
CNSv. 1.2refinement
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 3→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2993 -RANDOM
Rwork0.251 ---
all-54491 --
obs-42405 99.6 %-
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9310 0 10 0 9320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.607
X-RAY DIFFRACTIONc_bond_d0.0093
LS refinement shellHighest resolution: 3 Å

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