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- PDB-7al5: Crystal structure of the selenomethionine substituted hypothetica... -

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Basic information

Entry
Database: PDB / ID: 7al5
TitleCrystal structure of the selenomethionine substituted hypothetical protein PA1622 from Pseudomonas aeruginosa PAO1
ComponentsProbable hydrolase
KeywordsUNKNOWN FUNCTION / Esterase fold / hypothetical protein / Pseudomonas aeruginosa PAO1 / possible drug target / selenomethionine / Alpha/Beta hydrolase fold / Putative lipolytic enzyme
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Probable hydrolase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.42 Å
AuthorsFeiler, C.G. / Blankenfeldt, W.
CitationJournal: To Be Published
Title: Crystal structure of the selenomethionine substituted hypothetical protein PA1622 from Pseudomonas aeruginosa PAO1
Authors: Feiler, C.G. / Blankenfeldt, W.
History
DepositionOct 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Probable hydrolase
B: Probable hydrolase
C: Probable hydrolase
D: Probable hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,1679
Polymers126,6504
Non-polymers5175
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-68 kcal/mol
Surface area43510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.308, 136.308, 148.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Probable hydrolase


Mass: 31662.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA1622 / Plasmid: P10$ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I3A0

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Non-polymers , 5 types, 572 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES pH7 5% PEG 6000 / PH range: 6.8 - 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.42→19.93 Å / Num. obs: 59611 / % possible obs: 99.6 % / Redundancy: 22.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.43 / Rpim(I) all: 0.094 / Rrim(I) all: 0.45 / Net I/σ(I): 10.2
Reflection shellResolution: 2.42→2.48 Å / Rmerge(I) obs: 2.555 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4580 / CC1/2: 0.4 / Rpim(I) all: 0.633 / Rrim(I) all: 2.711 / Χ2: 1

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.42→19.93 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 2946 4.95 %
Rwork0.1638 --
obs0.1671 59516 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8747 0 34 569 9350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148977
X-RAY DIFFRACTIONf_angle_d1.7512167
X-RAY DIFFRACTIONf_dihedral_angle_d23.4621249
X-RAY DIFFRACTIONf_chiral_restr0.0661356
X-RAY DIFFRACTIONf_plane_restr0.0111581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.450.36831380.28392585X-RAY DIFFRACTION95
2.45-2.50.29791690.25222640X-RAY DIFFRACTION100
2.5-2.540.29141510.23532689X-RAY DIFFRACTION100
2.54-2.590.25011250.21932687X-RAY DIFFRACTION100
2.59-2.640.30421080.20792714X-RAY DIFFRACTION100
2.64-2.70.31481620.21072675X-RAY DIFFRACTION100
2.7-2.760.24971380.19942692X-RAY DIFFRACTION100
2.76-2.830.30031300.19242705X-RAY DIFFRACTION100
2.83-2.910.25071290.17282702X-RAY DIFFRACTION100
2.91-2.990.24791220.17572697X-RAY DIFFRACTION100
2.99-3.090.25331360.17052713X-RAY DIFFRACTION100
3.09-3.20.23031430.17422699X-RAY DIFFRACTION100
3.2-3.330.26581380.16852707X-RAY DIFFRACTION100
3.33-3.480.21471490.1482685X-RAY DIFFRACTION100
3.48-3.660.22161330.14232707X-RAY DIFFRACTION100
3.66-3.890.20931530.13612694X-RAY DIFFRACTION100
3.89-4.190.18341510.12512682X-RAY DIFFRACTION100
4.19-4.60.18281540.12092694X-RAY DIFFRACTION100
4.6-5.260.17191410.12182738X-RAY DIFFRACTION100
5.26-6.580.21021380.16332709X-RAY DIFFRACTION100
6.59-19.930.20511380.15672756X-RAY DIFFRACTION100

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