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- PDB-2yz2: Crystal structure of the ABC transporter in the cobalt transport ... -

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Basic information

Entry
Database: PDB / ID: 2yz2
TitleCrystal structure of the ABC transporter in the cobalt transport system
ComponentsPutative ABC transporter ATP-binding protein TM_0222
KeywordsHYDROLASE / ABC Transporter / Cobalt transport / ATP-binding protein / TM0222 / Inner membrane / Membrane / Nucleotide-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Translocases / riboflavin transport / riboflavin transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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 / P-loop containing nucleoside triphosphate hydrolase ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Energy-coupling factor transporter ATP-binding protein EcfA2
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsEthayathullah, A.S. / Bessho, Y. / Padmanabhan, B. / Singh, T.P. / Kaur, P. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the ABC transporter in the cobalt transport system
Authors: Ethayathullah, A.S. / Bessho, Y. / Padmanabhan, B. / Singh, T.P. / Kaur, P. / Yokoyama, S.
History
DepositionMay 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 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: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222


Theoretical massNumber of molelcules
Total (without water)60,5522
Polymers60,5522
Non-polymers00
Water8,575476
1
A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222

A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222

A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222

A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222


Theoretical massNumber of molelcules
Total (without water)242,2088
Polymers242,2088
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area20054.1 Å2
MethodPISA
2
A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222

A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222


Theoretical massNumber of molelcules
Total (without water)121,1044
Polymers121,1044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area8043.2 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.499, 148.499, 106.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Putative ABC transporter ATP-binding protein TM_0222 / Putative cobalt import ATP-binding protein cbiO 1


Mass: 30276.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL-X
References: UniProt: Q9WY65, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M potassium flouride, 20% (w/v) PEG 3350 (PEG/ION-2), pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97891, 0.90000, 0.97934
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978911
20.91
30.979341
ReflectionResolution: 2.3→50 Å / Num. all: 31565 / Num. obs: 31555 / % possible obs: 100 % / Observed criterion σ(F): -3 / Redundancy: 21.3 % / Rmerge(I) obs: 0.117
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.49 / Num. unique all: 3095 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.83 / SU B: 7.397 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29403 1467 5 %RANDOM
Rwork0.21352 ---
obs0.21751 27606 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.44 Å20 Å2
2--0.87 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 0 476 4699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224345
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9825859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5835532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73823.695203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07215812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8291536
X-RAY DIFFRACTIONr_chiral_restr0.1420.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023242
X-RAY DIFFRACTIONr_nbd_refined0.2360.22308
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22992
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2347
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.224
X-RAY DIFFRACTIONr_mcbond_it1.2641.52745
X-RAY DIFFRACTIONr_mcangle_it1.93424306
X-RAY DIFFRACTIONr_scbond_it3.12531801
X-RAY DIFFRACTIONr_scangle_it4.6684.51552
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 92 -
Rwork0.18 1525 -
obs--71.45 %

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