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- PDB-2pjz: The crystal structure of putative Cobalt transport ATP-binding pr... -

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Basic information

Entry
Database: PDB / ID: 2pjz
TitleThe crystal structure of putative Cobalt transport ATP-binding protein (cbiO-2), ST1066
ComponentsHypothetical protein ST1066
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ATP binding protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
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
ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHirata, K. / Hasegawa, K. / Ebihara, A. / Yamamoto, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: The crystal structure of putative Cobalt transport ATP-binding protein (cbiO-2), ST1066
Authors: Hirata, K. / Hasegawa, K. / Ebihara, A. / Yamamoto, M. / Yokoyama, S.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hypothetical protein ST1066
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8766
Polymers29,3961
Non-polymers4805
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical protein ST1066
hetero molecules

A: Hypothetical protein ST1066
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,75312
Polymers58,7922
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area4050 Å2
ΔGint-159.8 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.094, 102.094, 104.662
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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Components

#1: Protein Hypothetical protein ST1066 / putative Cobalt transport ATP-binding protein (cbiO-2)


Mass: 29396.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta834(DE3) / References: UniProt: Q972R9
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.5M Ammonium sulfate, 0.1M Sodium citrate tribasic dihydrate, pH5.6, 1.0M Lithium sulfate monohydrate, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.979 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 17, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 25918 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 21.6 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 53.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 21.4 % / Mean I/σ(I) obs: 10.12 / Num. unique all: 2524 / Rsym value: 0.292 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→24.8 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.981 / SU ML: 0.091 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24172 1316 5.1 %RANDOM
Rwork0.19586 ---
obs0.19821 24554 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.532 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 25 208 2344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222168
X-RAY DIFFRACTIONr_angle_refined_deg1.5492.0152936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3723.91392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25115425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4451517
X-RAY DIFFRACTIONr_chiral_restr0.1040.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021571
X-RAY DIFFRACTIONr_nbd_refined0.2170.21094
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2202
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.218
X-RAY DIFFRACTIONr_mcbond_it1.081.51381
X-RAY DIFFRACTIONr_mcangle_it1.74422135
X-RAY DIFFRACTIONr_scbond_it2.6723908
X-RAY DIFFRACTIONr_scangle_it3.9984.5792
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 93 -
Rwork0.184 1748 -
obs--99.62 %

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