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- PDB-4q63: Crystal Structure of Legionella Uncharacterized Protein Lpg0364 -

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Basic information

Entry
Database: PDB / ID: 4q63
TitleCrystal Structure of Legionella Uncharacterized Protein Lpg0364
ComponentsUncharacterized protein Lpg0364
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta / beta-barrel
Function / homology
Function and homology information


cyclic-di-GMP binding
Similarity search - Function
Thrombin, subunit H - #430 / PilZ domain / PilZ domain / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / FORMIC ACID / PilZ domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.953 Å
AuthorsKim, Y. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Legionella Uncharacterized Protein Lpg0364
Authors: Kim, Y. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Lpg0364
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,10410
Polymers12,3531
Non-polymers7529
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.117, 82.117, 38.689
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein Lpg0364


Mass: 12352.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg0364 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q5ZYK8

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Non-polymers , 5 types, 58 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M Cd Chloride, 0.1M HEPES pH7.5, 15%PEG400, 11%Etylen Glycol, 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: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 10988 / Num. obs: 10988 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.098 / Net I/σ(I): 11.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 524 / Rsym value: 0.857 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.953→28.158 Å / SU ML: 0.17 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.92 / Stereochemistry target values: ML / Details: number of reflections include Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1004 4.82 %random
Rwork0.183 ---
obs0.185 20849 98.47 %-
all-20849 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.2 Å2
Refinement stepCycle: LAST / Resolution: 1.953→28.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms763 0 16 49 828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007817
X-RAY DIFFRACTIONf_angle_d1.0161097
X-RAY DIFFRACTIONf_dihedral_angle_d15.951315
X-RAY DIFFRACTIONf_chiral_restr0.081126
X-RAY DIFFRACTIONf_plane_restr0.004142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9525-2.05550.23021490.27572753291296
2.0555-2.18420.30291490.23862786293597
2.1842-2.35280.2621240.20332844296898
2.3528-2.58940.21431600.18952864302499
2.5894-2.96370.21781520.187828493001100
2.9637-3.73260.20471300.178928933020100
3.7326-28.16060.21511400.16392856299699
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.8445-1.09350.76646.4936-1.31095.69770.3133-1.21520.25630.1065-0.03251.0485-0.3959-1.0186-0.14750.3719-0.10080.09740.6256-0.16910.3574-18.642441.5347-1.1458
24.10710.49792.93671.822-3.116410.10290.0213-0.6508-0.4568-0.2242-0.02960.02670.8472-0.44270.00160.3137-0.11250.05850.3511-0.01960.3434-12.311438.5120.9757
31.81332.2178-2.72792.7671-3.31513.99-0.0424-1.8925-2.74440.447-0.507-1.74251.28180.09830.34890.7322-0.0284-0.0920.64140.29990.946-2.777533.27166.1395
47.18711.63334.06064.42891.34325.03070.10640.5442-0.16320.0186-0.10170.24320.4346-0.2834-0.01710.2234-0.03970.04470.3933-0.02410.2057-9.626741.5442-4.5756
58.7892.30961.33847.0288-0.59647.8304-0.09210.10860.3349-0.2975-0.13690.7796-0.3102-0.81550.25970.29310.0084-0.02920.2691-0.08130.256-16.099546.7538-3.9454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 99 )

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