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- PDB-3lag: The crystal structure of a functionally unknown protein RPA4178 f... -

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Basic information

Entry
Database: PDB / ID: 3lag
TitleThe crystal structure of a functionally unknown protein RPA4178 from Rhodopseudomonas palustris CGA009
Componentsuncharacterized protein RPA4178
Keywordsstructural genomics / unknown function / functionally unknown protein / RPA4178 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / NICKEL (II) ION / Cupin_2 domain-containing protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsTan, K. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein RPA4178 from Rhodopseudomonas palustris CGA009
Authors: Tan, K. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
SupersessionFeb 2, 2010ID: 2OZI
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein RPA4178
B: uncharacterized protein RPA4178
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9078
Polymers21,6112
Non-polymers2966
Water6,359353
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-38 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.871, 59.243, 65.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. The A and B chains are likely to form a dimer.

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Components

#1: Protein uncharacterized protein RPA4178


Mass: 10805.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: PA4178 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6N272
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M CaCl2, 0.1M HEPES, 15% PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2006 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.15→29.6 Å / Num. all: 59329 / Num. obs: 59329 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 125.76
Reflection shellResolution: 1.15→1.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.36 / Num. unique all: 1790 / % possible all: 90

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→26.981 Å / SU ML: 0.14 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 2991 5.05 %random
Rwork0.1854 ---
all0.1871 59209 --
obs0.1871 59209 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.462 Å2 / ksol: 0.419 e/Å3
Refinement stepCycle: LAST / Resolution: 1.15→26.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1590 0 12 354 1956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081643
X-RAY DIFFRACTIONf_angle_d1.1882251
X-RAY DIFFRACTIONf_dihedral_angle_d16.112642
X-RAY DIFFRACTIONf_chiral_restr0.075257
X-RAY DIFFRACTIONf_plane_restr0.005299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1504-1.19160.26132640.2345293X-RAY DIFFRACTION94
1.1916-1.23930.25553470.20935541X-RAY DIFFRACTION100
1.2393-1.29570.22862780.18985613X-RAY DIFFRACTION100
1.2957-1.3640.22013000.17965618X-RAY DIFFRACTION100
1.364-1.44940.21283220.16925617X-RAY DIFFRACTION100
1.4494-1.56130.20582770.15435672X-RAY DIFFRACTION100
1.5613-1.71840.20732760.15295669X-RAY DIFFRACTION100
1.7184-1.9670.18823200.15695697X-RAY DIFFRACTION100
1.967-2.4780.20352900.17185734X-RAY DIFFRACTION100
2.478-26.98880.23713170.2115764X-RAY DIFFRACTION97

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