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- PDB-4wrp: The C-terminal domain of gene product lpg0944 from Legionella pne... -

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Basic information

Entry
Database: PDB / ID: 4wrp
TitleThe C-terminal domain of gene product lpg0944 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Effector proteins / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology: / RavJ, Peptidase domain / Domain of unknown function DUF5617 / Domain of unknown function (DUF5617) / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Evdokimova, E. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: The C-terminal domain of gene product lpg0944 from Legionella pneumophila subsp. pneumophila str. Philadelphia 1.
Authors: Cuff, M.E. / Evdokimova, E. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,8322
Polymers28,8322
Non-polymers00
Water3,405189
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,4161
Polymers14,4161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,4161
Polymers14,4161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.352, 60.714, 57.523
Angle α, β, γ (deg.)90.000, 104.610, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Uncharacterized protein


Mass: 14416.233 Da / Num. of mol.: 2 / Fragment: Residues 251-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0944 / Plasmid: p15Tv / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5ZWY9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 2.8M NaCl 0.1M Tris-HCl pH8.5 2% MPD / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 18, 2011
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Number: 99589 / Rmerge(I) obs: 0.066 / Χ2: 1.44 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 22416 / % possible obs: 97.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.165010.064.1454.1
4.095.1610.0452.7674.4
3.584.0910.0512.5524.4
3.253.5810.0542.5474.5
3.023.2510.0612.0374.5
2.843.0210.0651.7134.6
2.72.8410.071.5534.6
2.582.710.0791.2214.7
2.482.5810.0921.1654.7
2.392.4810.11.0814.7
2.322.3910.1180.9854.7
2.252.3210.1240.9024.7
2.192.2510.1410.824.7
2.142.1910.1580.8424.7
2.092.1410.1880.7944.7
2.052.0910.2120.7694.6
2.012.0510.2580.7644.5
1.972.0110.3070.7344.2
1.931.9710.3060.6993.7
1.91.9310.4020.6673.4
ReflectionResolution: 1.9→50 Å / Num. all: 22416 / Num. obs: 22416 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.438 / Net I/av σ(I): 28.28 / Net I/σ(I): 10.8 / Num. measured all: 99589
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.933.40.40210540.66795.5
1.93-1.973.70.30611100.69995.5
1.97-2.014.20.30710870.73497.3
2.01-2.054.50.25811100.76497.9
2.05-2.094.60.21211100.76997.1
2.09-2.144.70.18811430.79498.9
2.14-2.194.70.15810970.84298.1
2.19-2.254.70.14111380.8298
2.25-2.324.70.12411170.90298.5
2.32-2.394.70.11811310.98598.7
2.39-2.484.70.111111.08198.7
2.48-2.584.70.09211401.16598.8
2.58-2.74.70.07911311.22198.9
2.7-2.844.60.0711161.55398.9
2.84-3.024.60.06511431.71398.9
3.02-3.254.50.06111432.03799.1
3.25-3.584.50.05411392.54799.2
3.58-4.094.40.05111342.55298.5
4.09-5.164.40.04511472.76798.5
5.16-504.10.0611154.14592.8

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Phasing

PhasingMethod: SAD
Phasing MAD setHighest resolution: 2.45 Å / Lowest resolution: 50 Å
Phasing MAD set shell
IDResolution (Å)
114.59-50
18.54-14.59
16.04-8.54
14.67-6.04
13.81-4.67
13.21-3.81
12.78-3.21
12.45-2.78
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
119.19110.2730.1880.0833.638
224.31890.2740.055-0.4112.23
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
14.59-500.2070.241036315
8.54-14.590.2890.328016914920
6.04-8.540.3580.401046441450
4.67-6.040.3790.412083276567
3.81-4.670.3540.37601291121675
3.21-3.810.320.33601870178090
2.78-3.210.3180.333025592446113
2.45-2.780.2530.263033343209125
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 19894
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.55-10079.30.325518
5.29-6.5565.20.732503
4.65-5.2966.70.826505
4.23-4.6565.10.843518
3.91-4.2363.10.825534
3.65-3.9168.30.822579
3.44-3.6568.70.816641
3.27-3.4463.90.827657
3.11-3.2768.60.805670
2.98-3.11660.803735
2.86-2.9865.30.812744
2.76-2.8667.10.812789
2.66-2.7668.90.82820
2.58-2.6669.90.796825
2.5-2.5871.70.812853
2.43-2.578.60.8899
2.37-2.4389.30.76916
2.31-2.3788.40.776910
2.25-2.3188.90.766906
2.2-2.2590.80.753871
2.15-2.291.90.712852
2.1-2.1587.50.724813
2.06-2.187.80.652780
2.02-2.0687.50.638748
1.98-2.02930.516725
1.95-1.9890.9688
1.9-1.9592.40.39895

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Processing

Software
NameVersionClassification
HKL-3000data reduction
MLPHAREphasing
DM6.1phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.5 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2088 / WRfactor Rwork: 0.1609 / FOM work R set: 0.7699 / SU B: 8.494 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1315 / SU Rfree: 0.1279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 1107 4.9 %RANDOM
Rwork0.1623 21282 --
obs0.1645 21282 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.04 Å2 / Biso mean: 38.9 Å2 / Biso min: 19.23 Å2
Baniso -1Baniso -2Baniso -3
1-6.9 Å2-0 Å2-1.35 Å2
2---4.45 Å2-0 Å2
3----1.54 Å2
Refinement stepCycle: final / Resolution: 1.9→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 0 189 2146
Biso mean---48.02 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192043
X-RAY DIFFRACTIONr_bond_other_d0.0020.021920
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9012771
X-RAY DIFFRACTIONr_angle_other_deg0.84834370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05122.92113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75315335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3221519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022339
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
X-RAY DIFFRACTIONr_mcbond_it1.8622.366956
X-RAY DIFFRACTIONr_mcbond_other1.8632.365955
X-RAY DIFFRACTIONr_mcangle_it2.8133.5251195
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 76 -
Rwork0.271 1503 -
all-1579 -
obs--95.64 %
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)
10.93090.39270.33513.8317-0.95081.4446-0.01910.11140.0299-0.2134-0.0376-0.17690.00580.08970.05670.0158-0.00930.01570.11430.00720.06814.291337.206254.3237
20.58340.32470.11432.57770.81322.0605-0.01620.0338-0.00480.16050.02880.14570.0265-0.1865-0.01260.0343-0.00690.01790.14460.01980.079414.780338.329181.4613
30.57331.7503-2.3685.8181-6.870210.11310.0073-0.0962-0.1074-0.1825-0.2589-0.4866-0.31870.39040.25160.2317-0.01480.08660.2564-0.01230.2804-1.69638.859979.2755
43.3988-0.0587-1.28579.95684.89883.06910.1080.06160.1317-0.2023-0.23110.0971-0.1771-0.36910.12310.02070.0651-0.00170.3293-0.07910.196717.690870.1647109.2409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A251 - 356
2X-RAY DIFFRACTION2B251 - 356
3X-RAY DIFFRACTION3A357 - 371
4X-RAY DIFFRACTION4B363 - 372

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