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- PDB-5x41: 3.5A resolution structure of a cobalt energy-coupling factor tran... -

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Basic information

Entry
Database: PDB / ID: 5x41
Title3.5A resolution structure of a cobalt energy-coupling factor transporter using LCP method-CbiMQO
Components
  • Cobalt ABC transporter ATP-binding protein
  • Cobalt transport protein CbiM
  • Uncharacterized protein CbiQ
KeywordsTRANSPORT PROTEIN / CbiMQO / ECF transporter / LCP
Function / homology
Function and homology information


cobalt ion transport / cobalt ion transmembrane transporter activity / cobalamin biosynthetic process / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding
Similarity search - Function
Cobalt ECF transporter T component CbiQ / Cobalamin (vitamin B12) transport protein CbiM / : / Cobalt transport protein ATP-binding subunit / Metal transport protein CbiM/NikMN / Cobalt uptake substrate-specific transmembrane region / ABC/ECF transporter, transmembrane component / Cobalt transport protein / : / ABC transporter, CbiO/EcfA subunit ...Cobalt ECF transporter T component CbiQ / Cobalamin (vitamin B12) transport protein CbiM / : / Cobalt transport protein ATP-binding subunit / Metal transport protein CbiM/NikMN / Cobalt uptake substrate-specific transmembrane region / ABC/ECF transporter, transmembrane component / Cobalt transport protein / : / ABC transporter, CbiO/EcfA subunit / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cobalt transport protein CbiM / Cobalt/nickel transport system permease protein / ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.47 Å
AuthorsBao, Z. / Qi, X. / Zhao, W. / Li, D. / Zhang, P.
CitationJournal: Cell Res. / Year: 2017
Title: Structure and mechanism of a group-I cobalt energy coupling factor transporter
Authors: Bao, Z. / Qi, X. / Hong, S. / Xu, K. / He, F. / Zhang, M. / Chen, J. / Chao, D. / Zhao, W. / Li, D. / Wang, J. / Zhang, P.
History
DepositionFeb 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cobalt ABC transporter ATP-binding protein
B: Cobalt ABC transporter ATP-binding protein
M: Cobalt transport protein CbiM
Q: Uncharacterized protein CbiQ
C: Cobalt ABC transporter ATP-binding protein
D: Cobalt ABC transporter ATP-binding protein
E: Cobalt transport protein CbiM
F: Uncharacterized protein CbiQ


Theoretical massNumber of molelcules
Total (without water)217,4228
Polymers217,4228
Non-polymers00
Water00
1
A: Cobalt ABC transporter ATP-binding protein
B: Cobalt ABC transporter ATP-binding protein
M: Cobalt transport protein CbiM
Q: Uncharacterized protein CbiQ


Theoretical massNumber of molelcules
Total (without water)108,7114
Polymers108,7114
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-101 kcal/mol
Surface area41440 Å2
MethodPISA
2
C: Cobalt ABC transporter ATP-binding protein
D: Cobalt ABC transporter ATP-binding protein
E: Cobalt transport protein CbiM
F: Uncharacterized protein CbiQ


Theoretical massNumber of molelcules
Total (without water)108,7114
Polymers108,7114
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12990 Å2
ΔGint-101 kcal/mol
Surface area41300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.159, 135.040, 204.424
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
Cobalt ABC transporter ATP-binding protein / CbiO


Mass: 29464.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7HZ57*PLUS
#2: Protein Cobalt transport protein CbiM / Energy-coupling factor transporter probable substrate-capture protein CbiM / ECF transporter S component CbiM


Mass: 22554.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: cbiM / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q0R232
#3: Protein Uncharacterized protein CbiQ


Mass: 27228.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1G7HYD7*PLUS

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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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 0.1M NaCl, 35-48% PEG 400, 0.1M MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.47→50 Å / Num. obs: 34336 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data processing
RefinementResolution: 3.47→47.962 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3353 1727 5.04 %
Rwork0.2986 --
obs0.3005 34286 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.47→47.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14359 0 0 0 14359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01514586
X-RAY DIFFRACTIONf_angle_d3.17419868
X-RAY DIFFRACTIONf_dihedral_angle_d19.8825208
X-RAY DIFFRACTIONf_chiral_restr0.2012464
X-RAY DIFFRACTIONf_plane_restr0.0142527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4702-3.57220.36691210.36042253X-RAY DIFFRACTION82
3.5722-3.68750.37281270.34722704X-RAY DIFFRACTION99
3.6875-3.81920.36961460.32572688X-RAY DIFFRACTION98
3.8192-3.97210.41541650.33652704X-RAY DIFFRACTION99
3.9721-4.15280.34691510.31622697X-RAY DIFFRACTION99
4.1528-4.37160.30441360.30372756X-RAY DIFFRACTION99
4.3716-4.64520.35111480.29992733X-RAY DIFFRACTION100
4.6452-5.00360.3131350.30712778X-RAY DIFFRACTION99
5.0036-5.50640.35621680.32072721X-RAY DIFFRACTION99
5.5064-6.30170.41360.32792798X-RAY DIFFRACTION99
6.3017-7.93370.36131360.29482827X-RAY DIFFRACTION99
7.9337-47.96660.26441580.23712900X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -75.523 Å / Origin y: 129.1001 Å / Origin z: 425.3314 Å
111213212223313233
T0.7303 Å20.0765 Å2-0.0652 Å2-0.5176 Å2-0.0419 Å2--0.881 Å2
L1.0054 °20.5986 °20.1941 °2-0.5714 °20.2092 °2--0.213 °2
S-0.1165 Å °0.0587 Å °0.2241 Å °-0.0512 Å °0.079 Å °0.0752 Å °-0.1281 Å °0.0306 Å °0.0122 Å °
Refinement TLS groupSelection details: all

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