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- PDB-5x3x: 2.8A resolution structure of a cobalt energy-coupling factor tran... -

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Basic information

Entry
Database: PDB / ID: 5x3x
Title2.8A resolution structure of a cobalt energy-coupling factor transporter-CbiMQO
Components
  • Cobalt ABC transporter ATP-binding protein
  • Cobalt transport protein CbiM
  • Uncharacterized protein CbiQ
KeywordsTRANSPORT PROTEIN / Complex / ECF transporter
Function / homology
Function and homology information


Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / 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 transport protein CbiQ / Cobalt transport protein CbiM / Cobalt import ATP-binding protein CbiO
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.788 Å
AuthorsBao, Z. / Qi, X. / Wang, J. / 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 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Structure summary
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Mar 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

Downloads & links

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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
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)214,7518
Polymers214,7518
Non-polymers00
Water2,630146
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)107,3764
Polymers107,3764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)107,3764
Polymers107,3764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.676, 220.564, 301.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: O68106*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, UniProt: D5AUZ9*PLUS
#3: Protein Uncharacterized protein CbiQ


Mass: 25892.801 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: D5AUZ7*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1M ammonium sulfate, 0.1M ADA, pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Nov 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 51793 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data processing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.788→48.334 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 2376 5.1 %
Rwork0.2141 --
obs0.2159 46628 87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.788→48.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14820 0 0 146 14966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01515036
X-RAY DIFFRACTIONf_angle_d1.77120480
X-RAY DIFFRACTIONf_dihedral_angle_d15.495368
X-RAY DIFFRACTIONf_chiral_restr0.0912522
X-RAY DIFFRACTIONf_plane_restr0.0132610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7882-2.84510.278460.2496833X-RAY DIFFRACTION28
2.8451-2.9070.3146780.26841467X-RAY DIFFRACTION50
2.907-2.97460.3113980.25951828X-RAY DIFFRACTION62
2.9746-3.04890.33431100.25862223X-RAY DIFFRACTION75
3.0489-3.13140.27941420.26142540X-RAY DIFFRACTION86
3.1314-3.22350.2881530.24582796X-RAY DIFFRACTION94
3.2235-3.32750.27051660.23222855X-RAY DIFFRACTION97
3.3275-3.44640.27771610.22682943X-RAY DIFFRACTION99
3.4464-3.58440.25511790.21242950X-RAY DIFFRACTION99
3.5844-3.74740.25021410.21122970X-RAY DIFFRACTION99
3.7474-3.94490.25611370.20482999X-RAY DIFFRACTION100
3.9449-4.19190.22321390.19012948X-RAY DIFFRACTION99
4.1919-4.51540.23061750.18032967X-RAY DIFFRACTION99
4.5154-4.96940.20461460.18762969X-RAY DIFFRACTION98
4.9694-5.68750.23911580.22042978X-RAY DIFFRACTION98
5.6875-7.16190.25831660.24092999X-RAY DIFFRACTION98
7.1619-48.34160.22691810.2052987X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 87.436 Å / Origin y: 134.2336 Å / Origin z: 413.0794 Å
111213212223313233
T0.2639 Å20.0121 Å2-0.0344 Å2-0.2741 Å2-0.0227 Å2--0.2624 Å2
L-0.0266 °2-0.0058 °2-0.0103 °2-0.0487 °20.1703 °2--0.4473 °2
S0.014 Å °-0.0052 Å °0.0118 Å °0.0372 Å °0.0205 Å °-0.0304 Å °0.0618 Å °0.0331 Å °-0.0529 Å °
Refinement TLS groupSelection details: all

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