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- PDB-3htr: Crystal Structure of PRC-barrel Domain Protein from Rhodopseudomo... -

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Basic information

Entry
Database: PDB / ID: 3htr
TitleCrystal Structure of PRC-barrel Domain Protein from Rhodopseudomonas palustris
Componentsuncharacterized PRC-barrel Domain Protein
Keywordsstructural genomics / unknown function / beta-barrel / photo-reaction-center domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


PRC-barrel domain / PRC-barrel domain / PRC-barrel domain / PRC-barrel-like superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / PRC domain-containing protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Kinney, J. / Babnigg, G. / Harwood, C. / Kerfeld, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of PRC-barrel Domain Protein from Rhodopseudomonas palustris
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Kinney, J. / Babnigg, G. / Harwood, C. / Kerfeld, C. / Joachimiak, A.
History
DepositionJun 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized PRC-barrel Domain Protein
B: uncharacterized PRC-barrel Domain Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0419
Polymers26,5992
Non-polymers4427
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-138 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.644, 63.061, 61.866
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein uncharacterized PRC-barrel Domain Protein


Mass: 13299.460 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA0009 / Gene: RPA4758 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: Q6N0K4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.86 Å3/Da / Density % sol: 33.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-tris-Propane pH 7.0, 1.3 M di-ammonium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.06→28.01 Å / Num. all: 11619 / Num. obs: 11619 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 29.25 Å2 / Rsym value: 0.108 / Net I/σ(I): 7.4
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 604 / Rsym value: 0.348 / % possible all: 78

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
PHENIXmodel building
SOLVEphasing
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.4_58)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.06→28.01 Å / SU ML: 0.24 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1125 10 %RANDOM
Rwork0.193 ---
all0.197 11254 --
obs0.197 11254 92.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.044 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-25.4896 Å2-0 Å214.0719 Å2
2---15.9436 Å20 Å2
3----9.5461 Å2
Refinement stepCycle: LAST / Resolution: 2.06→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 16 56 1554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_deg1.379
X-RAY DIFFRACTIONf_dihedral_angle_d16.46
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0566-2.15010.25331160.22891059117577
2.1501-2.26350.28951260.23881116124282
2.2635-2.40520.28371330.23271197133089
2.4052-2.59080.27171490.22351330147996
2.5908-2.85130.26341450.21261350149597
2.8513-3.26330.26671460.19281337148399
3.2633-4.10940.19761480.17061361150999
4.1094-28.01610.19361620.17141379154199
Refinement TLS params.

S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3457-0.009-0.33790.80750.5021.32720.03880.010.01830.32490.02090.08780.0739-0.0040.2004-0.0054-0.01720.2463-0.0270.2451-8.02227.23553.2163
20.4129-0.3146-0.19181.21990.60371.6122-0.05690.0038-0.0332-0.13380.0063-0.07240.33250.03490.32430.01770.02690.269-0.00860.3067-5.518611.050737.2694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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