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- PDB-4ezi: Crystal structure of a putative hydrolase (lpg1103) from Legionel... -

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Basic information

Entry
Database: PDB / ID: 4ezi
TitleCrystal structure of a putative hydrolase (lpg1103) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.15 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / alpha-beta hydrolases fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
434 Repressor (Amino-terminal Domain) - #160 / Lipase, secreted / 434 Repressor (Amino-terminal Domain) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Alpha/beta hydrolase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (lpg1103) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 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 1.4Oct 16, 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4083
Polymers43,2661
Non-polymers1422
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.875, 63.488, 114.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 43266.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg1103 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5ZWI2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 28-403) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 28-403) 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.20M sodium acetate, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97916
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 16, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.15→28.637 Å / Num. all: 131916 / Num. obs: 131916 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 9.254 Å2 / Rsym value: 0.106 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.15-1.184.70.78714531896370.78799.3
1.18-1.214.70.6711.14420393540.67199.5
1.21-1.254.70.5881.34324191370.58899.8
1.25-1.294.80.5011.54215288670.50199.8
1.29-1.334.80.4221.84100586320.42299.9
1.33-1.384.80.36823983383810.36899.9
1.38-1.434.80.3182.33862980780.318100
1.43-1.494.80.2642.73727377690.264100
1.49-1.554.80.2133.43612374990.213100
1.55-1.634.80.1754.13468671530.175100
1.63-1.724.90.1534.63319368290.153100
1.72-1.824.90.135.33156064670.13100
1.82-1.954.90.11362972960750.113100
1.95-2.14.90.0976.92784656780.097100
2.1-2.35.90.0996.53080052550.099100
2.3-2.577.20.0986.73417347580.098100
2.57-2.978.60.0956.93633642460.095100
2.97-3.648.40.0837.73038536100.083100
3.64-5.1580.0758.72277628470.075100
5.15-28.6377.40.0847.81211116440.08499

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→28.637 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.002 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.032
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. POLYETHYLENE GLYCOL (PEG) AND CHLORIDE (CL) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1574 6631 5 %RANDOM
Rwork0.1354 ---
obs0.1365 131826 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.13 Å2 / Biso mean: 13.8875 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.15→28.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 8 536 3506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223292
X-RAY DIFFRACTIONr_bond_other_d0.0010.022214
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9624507
X-RAY DIFFRACTIONr_angle_other_deg0.95135439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8455416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14924.563160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78615541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8921511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213696
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02680
X-RAY DIFFRACTIONr_mcbond_it1.89831972
X-RAY DIFFRACTIONr_mcbond_other1.393778
X-RAY DIFFRACTIONr_mcangle_it2.69153221
X-RAY DIFFRACTIONr_scbond_it3.64281320
X-RAY DIFFRACTIONr_scangle_it5.188111269
X-RAY DIFFRACTIONr_rigid_bond_restr1.46435506
X-RAY DIFFRACTIONr_sphericity_free6.7483539
X-RAY DIFFRACTIONr_sphericity_bonded3.56835395
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 545 -
Rwork0.269 9084 -
all-9629 -
obs--99.22 %

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