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- PDB-2i9c: Crystal Structure of the Protein RPA1889 from Rhodopseudomonas pa... -

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Basic information

Entry
Database: PDB / ID: 2i9c
TitleCrystal Structure of the Protein RPA1889 from Rhodopseudomonas palustris CGA009
ComponentsHypothetical protein RPA1889
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SAD / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Domain of unknown function DUF2019 / Domain of unknown function (DUF2019) / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DUF2019 domain-containing protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsCymborowski, M.T. / Evdokimova, E. / Kagan, O. / Chruszcz, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Protein RPA1889 from Rhodopseudomonas palustris CGA009
Authors: Cymborowski, M.T. / Evdokimova, E. / Kagan, O. / Chruszcz, M. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionSep 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 5, 2011Group: Structure summary
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein RPA1889
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0213
Polymers13,9031
Non-polymers1182
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.022, 78.022, 38.979
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-160-

HOH

21A-164-

HOH

31A-170-

HOH

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Components

#1: Protein Hypothetical protein RPA1889


Mass: 13903.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA1889 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD (DE3) / References: UniProt: Q6N8L4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% Tascimate, 10% PEG5000 MME, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97904 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2→67.57 Å / Num. all: 9484 / Num. obs: 9449 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.057
Reflection shellResolution: 2→2.02 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 6.83 / Num. unique all: 206 / Rsym value: 0.298 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
CCP4phasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
Omodel building
RefinementMethod to determine structure: SAD / Resolution: 2→33.79 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.984 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: COOT HAS ALSO BEEN A SOFTWARE USED IN THE REFINEMENT. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20189 451 4.8 %RANDOM
Rwork0.17472 ---
obs0.17603 8989 99.73 %-
all-9449 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.113 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms929 0 8 92 1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022984
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9821339
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01825.43546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60115176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.223156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02748
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2486
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2689
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2541.5650
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5582999
X-RAY DIFFRACTIONr_scbond_it3.6223375
X-RAY DIFFRACTIONr_scangle_it4.7794.5334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 31 -
Rwork0.197 663 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: -14.168 Å / Origin y: 45.495 Å / Origin z: 2.91 Å
111213212223313233
T-0.175 Å2-0.0681 Å20.0121 Å2--0.052 Å2-0.0116 Å2---0.0556 Å2
L1.0989 °20.4093 °2-0.0113 °2-1.8961 °20.4471 °2--4.2714 °2
S-0.0018 Å °0.1088 Å °0.0373 Å °-0.0876 Å °0.1436 Å °0.0793 Å °-0.3067 Å °0.514 Å °-0.1418 Å °

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