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- PDB-3op6: Crystal structure of an oligo-nucleotide binding protein (lpg1207... -

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Basic information

Entry
Database: PDB / ID: 3op6
TitleCrystal structure of an oligo-nucleotide binding protein (lpg1207) from Legionella pneumophila subsp. pneumophila str. philadelphia 1 at 2.00 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / OLIGO-NUCLEOTIDE BINDING PROTEIN
Function / homologyYbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / aminoacyl-tRNA deacylase activity / Alpha-Beta Complex / Alpha Beta / YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an oligo-nucleotide binding protein (lpg1207) from Legionella pneumophila subsp. pneumophila str. philadelphia 1 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
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 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / software
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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6594
Polymers33,5352
Non-polymers1242
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-6 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.005, 63.828, 84.986
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC STATE IN SOLUTION.

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Components

#1: Protein Uncharacterized protein


Mass: 16767.559 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: lpg1207 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5ZW80
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4000M Na3Citrate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97927,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 23, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979271
30.979131
ReflectionResolution: 2→29.877 Å / Num. all: 20475 / Num. obs: 20475 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 25.097 Å2 / Rsym value: 0.114 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.053.60.7471542714930.747100
2.05-2.113.70.6521.2523814350.652100
2.11-2.173.60.5391.4517814270.539100
2.17-2.243.70.4311.8498713660.431100
2.24-2.313.60.3911.9485913380.391100
2.31-2.393.60.3352.2466812840.335100
2.39-2.483.60.2982.6457512580.298100
2.48-2.583.60.2543440312110.254100
2.58-2.73.60.2123.5416011500.212100
2.7-2.833.60.2023.7403411060.202100
2.83-2.983.60.1484.9384610610.148100
2.98-3.163.60.103736009970.103100
3.16-3.383.60.0768.934579630.07699.9
3.38-3.653.60.0669.731168680.066100
3.65-43.60.05611.329168160.05699.9
4-4.473.60.04912.726997540.04999.8
4.47-5.163.50.0511223156550.05199.6
5.16-6.323.50.05111.820075780.05199.5
6.32-8.943.40.04513.715164500.04599
8.94-29.87730.04113.58082650.04196.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2→29.877 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9143 / Occupancy max: 1 / Occupancy min: 0.15 / 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. 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT CONDITION IS MODELED INTO THE STRUCTURE. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4, NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1047 5.12 %RANDOM
Rwork0.1951 ---
obs0.1969 20430 --
Displacement parametersBiso max: 111.25 Å2 / Biso mean: 40.8756 Å2 / Biso min: 8.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.635 Å20 Å20 Å2
2---0.2535 Å20 Å2
3----1.3815 Å2
Refinement stepCycle: LAST / Resolution: 2→29.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 8 161 2334
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d785SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes333HARMONIC5
X-RAY DIFFRACTIONt_it2258HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion306SEMIHARMONIC5
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_contact2772SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2258HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3060HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion16.86
LS refinement shellResolution: 2→2.11 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2359 163 5.58 %
Rwork0.2116 2759 -
all0.213 2922 -
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)
14.0488-0.24381.50890.2763-0.07641.79080.00290.13240.0454-0.0119-0.018-0.0097-0.0472-0.04270.0151-0.21980.02710.01390.3058-0.0189-0.2492-36.152333.1755-4.1069
22.130.1579-1.41691.2663-0.75953.5437-0.01750.17230.0291-0.11720.0650.15840.0314-0.2767-0.0475-0.25760.0057-0.00490.3028-0.0196-0.2325-66.303136.5536-20.3087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 151
2X-RAY DIFFRACTION2{ B|* }B1 - 151

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