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- PDB-4jx2: Crystal structure of a putative secreted protein (lpg1979) from L... -

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Basic information

Entry
Database: PDB / ID: 4jx2
TitleCrystal structure of a putative secreted protein (lpg1979) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.65 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / ORFan protein / new combination of alpha helixes and beta sheets / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #2710 / Domain of unknown function DUF5624 / Domain of unknown function (DUF5624) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DUF5624 domain-containing protein
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 a hypothetical protein (lpg1979) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 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: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,87927
Polymers97,9862
Non-polymers2,89325
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16410 Å2
ΔGint-244 kcal/mol
Surface area32350 Å2
MethodPISA
2
A: hypothetical protein
B: hypothetical protein
hetero molecules

A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,75854
Polymers195,9724
Non-polymers5,78650
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area36770 Å2
ΔGint-506 kcal/mol
Surface area60750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.943, 145.086, 63.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein hypothetical protein


Mass: 48992.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg1979, YP_095995.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5ZU29

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Non-polymers , 6 types, 282 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (22-375) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (22-375) 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M lithium sulfate, 40.0% polyethylene glycol 400, 0.2M lithium sulfate, 40.0% polyethylene glycol 400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97932,0.91837,0.97858
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.918371
30.978581
ReflectionResolution: 2.65→47.97 Å / Num. obs: 33147 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.91 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.65-2.740.572.39677306497.5
2.74-2.850.419311528333599.7
2.85-2.980.3044.111472331099.1
2.98-3.140.2235.511550335498.7
3.14-3.340.145811370337398.9
3.34-3.590.110.810019316196.6
3.59-3.950.07115.211520334299.2
3.95-4.520.05119.711471335598.4
4.52-5.670.04720.810553327896.4
5.670.03925.311382355496.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.65→47.97 Å / Cor.coef. Fo:Fc: 0.9496 / Cor.coef. Fo:Fc free: 0.9231 / Occupancy max: 1 / Occupancy min: 0.75 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PEG FRAGMENTS, CL AND SO4 MODELED ARE PRESENT IN CRYSTALLIZATION CONDITION. 5.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 1683 5.08 %RANDOM
Rwork0.1622 ---
obs0.1642 33107 98.19 %-
Displacement parametersBiso max: 157.17 Å2 / Biso mean: 49.4094 Å2 / Biso min: 19.43 Å2
Baniso -1Baniso -2Baniso -3
1--4.6184 Å20 Å20 Å2
2--4.5879 Å20 Å2
3---0.0305 Å2
Refine analyzeLuzzati coordinate error obs: 0.285 Å
Refinement stepCycle: LAST / Resolution: 2.65→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 172 257 6770
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3021SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes173HARMONIC2
X-RAY DIFFRACTIONt_gen_planes918HARMONIC5
X-RAY DIFFRACTIONt_it6652HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion875SEMIHARMONIC5
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_contact8004SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6652HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9018HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion2.94
LS refinement shellResolution: 2.65→2.73 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2642 137 4.94 %
Rwork0.2056 2639 -
all0.2084 2776 -
obs--98.19 %
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)
14.91610.93632.02416.712-1.4660.0608-0.0117-0.22580.45890.13190.01680.4948-0.1076-0.1306-0.0051-0.0878-0.10320.0487-0.1796-0.08120.026693.5688-26.486158.014
21.0677-0.2072-0.02691.37220.23360.7297-0.0241-0.14750.08370.13160.02480.03360.0144-0.1549-0.0007-0.05410.0203-0.0053-0.02650.0255-0.1719104.05512.086980.8519
35.471-0.7510.59212.85771.14450-0.02510.1218-0.25590.00080.13070.29740.1632-0.1095-0.1055-0.01830.0623-0.0478-0.16430.02030.003993.096323.966872.4754
40.63670.3232-0.03191.590.17950.58110.00080.1207-0.1452-0.1937-0.0149-0.03120.0649-0.13310.0141-0.0427-0.0273-0.0196-0.0293-0.0007-0.128106.832-12.53252.4973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|50 - 91}A50 - 91
2X-RAY DIFFRACTION2{A|96 - 455}A96 - 455
3X-RAY DIFFRACTION3{B|50 - 91}B50 - 91
4X-RAY DIFFRACTION4{B|99 - 455}B99 - 455

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