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- PDB-5cnl: Crystal structure of an IcmL-like type IV secretion system protei... -

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Basic information

Entry
Database: PDB / ID: 5cnl
TitleCrystal structure of an IcmL-like type IV secretion system protein (lpg0120) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.65 A resolution
ComponentsIcmL-like
KeywordsPROTEIN TRANSPORT / type IV secretion system / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyType-IV b secretion system, inner-membrane complex component / Type-IV b secretion system, inner-membrane complex component / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / IcmL-like
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an IcmL-like type IV secretion system protein (lpg0120) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IcmL-like
B: IcmL-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,04215
Polymers34,6112
Non-polymers1,43113
Water41423
1
A: IcmL-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,29810
Polymers17,3051
Non-polymers9939
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IcmL-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7445
Polymers17,3051
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: IcmL-like
B: IcmL-like
hetero molecules

A: IcmL-like
B: IcmL-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,08430
Polymers69,2214
Non-polymers2,86326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area9030 Å2
ΔGint-221 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.381, 83.381, 221.829
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-207-

SO4

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Components

#1: Protein IcmL-like


Mass: 17305.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0120 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5ZZ91
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (23-176) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (23-176) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085M HEPES pH 7.5, 15% glycerol, 1.7% polyethylene glycol 400, 1.7M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.9793,0.9791
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 25, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.97931
30.97911
ReflectionResolution: 2.65→29.018 Å / Num. all: 13863 / Num. obs: 13863 / % possible obs: 99.2 % / Redundancy: 14.1 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.155 / Rsym value: 0.149 / Net I/av σ(I): 4.786 / Net I/σ(I): 14.6 / Num. measured all: 194866
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
2.65-2.7214.51.3571.310.6144569950.3521.3571.3112.399
2.72-2.7914.41.1181.0790.7140449750.291.1181.0792.899
2.79-2.8714.51.0130.9780.8137249450.2621.0130.978399.2
2.87-2.9614.40.740.7151.1131539120.1920.740.7154.199.2
2.96-3.0614.50.5980.5781.3128328870.1550.5980.5785.199.2
3.06-3.1714.30.4660.451.7122788590.1220.4660.456.499
3.17-3.2914.30.3860.3732.1120438450.1010.3860.3737.699.6
3.29-3.4214.40.270.2613115228020.070.270.26110.699.4
3.42-3.5714.20.2030.1964110877810.0530.2030.19613.499.4
3.57-3.7514.30.1710.1654.6107237520.0450.1710.16515.899.3
3.75-3.9514.10.1350.135.8100797160.0360.1350.1319.599.4
3.95-4.1913.90.1070.1037.195456850.0280.1070.10323.399.4
4.19-4.4814.10.090.0868.389236340.0240.090.08628.199.4
4.48-4.8413.70.0750.0739.984516150.020.0750.0733199.6
4.84-5.313.70.0820.0798.676605590.0220.0820.07928.799.5
5.3-5.9313.60.0910.0888.269925140.0240.0910.08826.399.5
5.93-6.8413.40.0860.0838.661954630.0230.0860.08328.299.4
6.84-8.3812.70.0650.06210.351814090.0180.0650.06234.199.8
8.38-11.8512.10.0490.04711.839283250.0140.0490.04741.899.7
11.85-29.01810.80.0430.04114.320501900.0130.0430.04136.893

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALA3.3.20data scaling
SHARPphasing
SHELXphasing
BUSTER2.10.2refinement
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→29.018 Å / Cor.coef. Fo:Fc: 0.9464 / Cor.coef. Fo:Fc free: 0.9328 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. CONDITIONS. 3. PEG AND SO4 MODELED WERE PRESENT IN CRYO CONDITION. 4. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 690 4.98 %RANDOM
Rwork0.1917 ---
obs0.193 13863 98.89 %-
Displacement parametersBiso max: 180.13 Å2 / Biso mean: 69.9986 Å2 / Biso min: 34.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.5014 Å20 Å20 Å2
2---0.5014 Å20 Å2
3---1.0027 Å2
Refine analyzeLuzzati coordinate error obs: 0.401 Å
Refinement stepCycle: LAST / Resolution: 2.65→29.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 84 23 2287
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1026SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes314HARMONIC5
X-RAY DIFFRACTIONt_it2311HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion297SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2691SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2311HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3142HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion2.97
LS refinement shellResolution: 2.65→2.86 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2056 148 5.32 %
Rwork0.2216 2635 -
all0.2206 2783 -
obs--98.89 %
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)
12.15821.1016-0.12852.27170.17162.20330.19160.15360.20880.04550.0983-0.2019-0.1244-0.2495-0.2898-0.0005-0.10110.0054-0.09330.1637-0.09132.035711.472914.9664
21.25530.1324-0.42554.1793-2.02653.2891-0.0319-0.00530.30160.27210.38770.5661-0.4006-0.3946-0.3557-0.0981-0.06170.0957-0.10240.1381-0.097914.68288.028631.7039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - 160}A0 - 160
2X-RAY DIFFRACTION2{B|23 - 161}B23 - 161

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