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- PDB-4rd8: The crystal structure of a functionally-unknown protein from Legi... -

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Basic information

Entry
Database: PDB / ID: 4rd8
TitleThe crystal structure of a functionally-unknown protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyDomain of of unknown function DUF5636 / Family of unknown function (DUF5636) / DUF5636 domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsTan, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally-unknown protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Authors: Tan, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)55,8322
Polymers55,8322
Non-polymers00
Water6,107339
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)27,9161
Polymers27,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)27,9161
Polymers27,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.102, 65.824, 103.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIt is predicted that the chains A and B are monomers.

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Components

#1: Protein Uncharacterized protein


Mass: 27916.000 Da / Num. of mol.: 2 / Fragment: Residues 1-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: str. Philadelphia 1 / Gene: lpg1960 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5ZU48
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 0.014mg/ml chymotrypsin, 30% Jeffmine ED-2001, pH 7.0, 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: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2014 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.72→33 Å / Num. all: 48470 / Num. obs: 48470 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 6 % / Biso Wilson estimate: 22.04 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 31.6
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.36 / Num. unique all: 2396 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDBuilder/HKL3000phasing
MLPHAREBuilder/HKL3000phasing
DMBuilder/HKL3000model building
DENZOBuilder/HKL3000data reduction
SCALEPACKBuilder/HKL3000data scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMBuilder/HKL3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→32.912 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 2417 4.99 %random
Rwork0.1737 ---
obs0.175 48422 99.24 %-
all-48422 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→32.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 0 339 3732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063486
X-RAY DIFFRACTIONf_angle_d0.9934715
X-RAY DIFFRACTIONf_dihedral_angle_d14.1191335
X-RAY DIFFRACTIONf_chiral_restr0.071531
X-RAY DIFFRACTIONf_plane_restr0.005614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.75330.28481300.24152572X-RAY DIFFRACTION95
1.7533-1.79150.26771510.21782670X-RAY DIFFRACTION100
1.7915-1.83310.22241200.20652721X-RAY DIFFRACTION100
1.8331-1.8790.2621550.20532671X-RAY DIFFRACTION100
1.879-1.92980.23531410.19862667X-RAY DIFFRACTION100
1.9298-1.98660.24291700.19672688X-RAY DIFFRACTION100
1.9866-2.05070.23461350.1852703X-RAY DIFFRACTION100
2.0507-2.12390.22911650.17622687X-RAY DIFFRACTION100
2.1239-2.2090.19541740.17162667X-RAY DIFFRACTION100
2.209-2.30950.19871330.16852719X-RAY DIFFRACTION100
2.3095-2.43120.2151570.17982689X-RAY DIFFRACTION100
2.4312-2.58350.24621150.17992767X-RAY DIFFRACTION100
2.5835-2.78280.18571330.18552732X-RAY DIFFRACTION100
2.7828-3.06270.23441260.18542760X-RAY DIFFRACTION100
3.0627-3.50550.20311380.17952757X-RAY DIFFRACTION99
3.5055-4.41480.15061260.14252771X-RAY DIFFRACTION99
4.4148-32.9180.17461480.16162764X-RAY DIFFRACTION95
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)
13.2562-2.6759-3.16097.6522.22153.09660.2094-0.31140.03460.3704-0.21230.85230.1325-0.55230.04890.3336-0.06610.08710.41610.02420.392726.4046-2.389177.9599
21.47970.10640.30823.5486-1.30464.7794-0.02850.32630.3443-0.3969-0.1536-0.0869-0.45090.15590.120.28040.0294-0.02010.15790.04810.312839.591214.845161.226
32.9684-1.5845-0.21953.66410.29761.8370.05550.12640.1616-0.2053-0.03320.0707-0.1194-0.0696-0.01960.1006-0.011-0.01610.12810.00670.157641.59764.523566.4869
42.35750.38390.24414.2528-1.89064.6084-0.02170.33480.1471-0.7853-0.08860.26720.3184-0.18230.07040.25850.0556-0.03360.229-0.00060.229633.07033.912159.7979
56.2956-2.7659-0.48642.86851.82239.1504-0.4646-0.2415-0.08220.59490.4485-1.13030.61061.3385-0.07540.47010.0501-0.04650.4116-0.02390.493974.7733-10.157684.3621
62.08590.04720.42011.79610.63055.1179-0.0060.2691-0.0931-0.1203-0.0014-0.06760.11050.22760.00050.12890.02250.02190.099-0.00970.153566.8182-18.254460.9264
72.465-2.41380.25084.86190.241.2440.040.1420.1327-0.0988-0.0621-0.1954-0.02670.15350.0370.1002-0.0181-0.01120.1570.0020.110661.8587-10.542268.3712
81.7870.0666-0.02832.21341.65563.6837-0.04880.12250.2094-0.19570.1377-0.2955-0.34670.5527-0.08240.1913-0.0132-0.0070.20740.04430.206272.017-7.702766.4094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 158 )
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 218 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 22 )
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 84 )
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 158 )
8X-RAY DIFFRACTION8chain 'B' and (resid 159 through 217 )

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