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- PDB-6d6j: Crystal structure of HIT family hydrolase from Legionella pneumop... -

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Basic information

Entry
Database: PDB / ID: 6d6j
TitleCrystal structure of HIT family hydrolase from Legionella pneumophila Philadelphia 1
ComponentsHIT family hydrolase
KeywordsHYDROLASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HIT family hydrolase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of HIT family hydrolase from Legionella pneumophila Philadelphia 1
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIT family hydrolase
B: HIT family hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5108
Polymers27,2372
Non-polymers2736
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-50 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.510, 56.480, 83.300
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 HIT family hydrolase


Mass: 13618.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: hit, lpg2765 / Plasmid: LepnA.00754.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q5ZRW1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus screen, B6: 10% PEG 8.000, 20% EG: 30mM of each Sodium Fluoride, Sodium Bromide, Sodium iodide: 100mM MOPS/HEPES pH 7.5: LepnA.00754.a.B1 at 7.4mg/ml: cryo: ...Details: Molecular Dimensions Morpheus screen, B6: 10% PEG 8.000, 20% EG: 30mM of each Sodium Fluoride, Sodium Bromide, Sodium iodide: 100mM MOPS/HEPES pH 7.5: LepnA.00754.a.B1 at 7.4mg/ml: cryo: direct: tray 297411b6: puck hop6-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.35→46.748 Å / Num. obs: 57465 / % possible obs: 98.7 % / Redundancy: 16.52 % / Biso Wilson estimate: 8.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.025 / Rrim(I) all: 0.026 / Χ2: 1.002 / Net I/σ(I): 68.78 / Num. measured all: 949324 / Scaling rejects: 650
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.393.7680.1318.5236400.9830.1585.6
1.39-1.428.8060.12615.1440500.9930.13498.3
1.42-1.469.7250.10619.3240130.9950.11299
1.46-1.5111.1810.08724.7138660.9970.09199.4
1.51-1.5614.3410.07333.0938010.9990.07699.9
1.56-1.6115.3090.06140.1537150.9990.06499.9
1.61-1.6716.1990.05445.435390.9990.056100
1.67-1.7416.9450.04951.6134270.9990.051100
1.74-1.8217.7290.04360.28329210.044100
1.82-1.9118.6390.03673.78315310.037100
1.91-2.0119.4030.03184.75301410.032100
2.01-2.1320.1790.02897.93286010.029100
2.13-2.2820.7170.025110.95266210.026100
2.28-2.4621.1030.023117.45251710.024100
2.46-2.721.4350.023123.02231810.023100
2.7-3.0221.9450.021134.39211010.021100
3.02-3.4922.8520.02149.69187810.02100
3.49-4.2725.2780.019168.41159510.019100
4.27-6.0433.9610.019196.69127010.019100
6.04-46.74836.1870.021199.697450.9990.021100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3092)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
PHENIXphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.35→46.748 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.55
RfactorNum. reflection% reflection
Rfree0.1404 2088 3.63 %
Rwork0.126 --
obs0.1265 57450 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.75 Å2 / Biso mean: 12.1724 Å2 / Biso min: 3.75 Å2
Refinement stepCycle: final / Resolution: 1.35→46.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 6 387 2130
Biso mean--22.81 27.29 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.38140.171100.11943082319284
1.3814-1.4160.1341480.10373635378398
1.416-1.45430.11791440.09883634377899
1.4543-1.49710.1491440.0943672381699
1.4971-1.54540.1191420.094536823824100
1.5454-1.60060.1221380.093436923830100
1.6006-1.66470.13181350.098837223857100
1.6647-1.74050.12981210.113337373858100
1.7405-1.83220.14211210.119537223843100
1.8322-1.9470.14381500.120737403890100
1.947-2.09740.12351580.127237293887100
2.0974-2.30840.12741450.12837423887100
2.3084-2.64240.14571370.137337853922100
2.6424-3.32910.15411310.141738323963100
3.3291-46.77560.15491640.149439564120100

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