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- PDB-3om8: The crystal structure of a hydrolase from Pseudomonas aeruginosa PA01 -

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Basic information

Entry
Database: PDB / ID: 3om8
TitleThe crystal structure of a hydrolase from Pseudomonas aeruginosa PA01
ComponentsProbable hydrolase
KeywordsHYDROLASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


3-oxoadipate enol-lactonase activity / beta-ketoadipate pathway
Similarity search - Function
3-oxoadipate enol-lactonase 1/2 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsTan, K. / Chhor, G. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a hydrolase from Pseudomonas aeruginosa PA01
Authors: Tan, K. / Chhor, G. / Buck, K. / Joachimiak, A.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable hydrolase
B: Probable hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6646
Polymers57,1502
Non-polymers5154
Water2,126118
1
A: Probable hydrolase
B: Probable hydrolase
hetero molecules

A: Probable hydrolase
B: Probable hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,32912
Polymers114,3004
Non-polymers1,0298
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6920 Å2
ΔGint-8 kcal/mol
Surface area38630 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint2 kcal/mol
Surface area20480 Å2
MethodPISA
3
A: Probable hydrolase
hetero molecules

B: Probable hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6646
Polymers57,1502
Non-polymers5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y+1/2,-z+1/41
Buried area2880 Å2
ΔGint7 kcal/mol
Surface area19900 Å2
MethodPISA
4
A: Probable hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8323
Polymers28,5751
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: Probable hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8323
Polymers28,5751
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.529, 91.529, 283.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsExperimentally unknown. It is predicted that the molecule is monomeric.

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Components

#1: Protein Probable hydrolase


Mass: 28574.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA0480 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q9I638
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 118 / 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: 5.2 Å3/Da / Density % sol: 76.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M proline, 0.1M HEPES, 10% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.25→48.5 Å / Num. all: 56314 / Num. obs: 56314 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 21.1
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2 / Num. unique all: 2443 / % possible all: 84.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→48.231 Å / SU ML: 0.29 / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 2562 5.07 %random
Rwork0.1922 ---
all0.1937 50526 --
obs0.1937 50526 86.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.161 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.615 Å20 Å2-0 Å2
2--14.615 Å20 Å2
3----29.23 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 32 118 4136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064123
X-RAY DIFFRACTIONf_angle_d0.9775619
X-RAY DIFFRACTIONf_dihedral_angle_d18.8891461
X-RAY DIFFRACTIONf_chiral_restr0.059644
X-RAY DIFFRACTIONf_plane_restr0.004732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2497-2.33010.35532210.29593514X-RAY DIFFRACTION65
2.3301-2.42340.31251890.2693929X-RAY DIFFRACTION72
2.4234-2.53370.28572160.23854288X-RAY DIFFRACTION78
2.5337-2.66730.27072510.22544556X-RAY DIFFRACTION84
2.6673-2.83440.28642660.22534805X-RAY DIFFRACTION88
2.8344-3.05320.23782460.21245010X-RAY DIFFRACTION90
3.0532-3.36040.23722770.20575222X-RAY DIFFRACTION95
3.3604-3.84650.20633060.17865365X-RAY DIFFRACTION97
3.8465-4.84540.16872910.14175491X-RAY DIFFRACTION98
4.8454-48.2420.19892990.18175784X-RAY DIFFRACTION97
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)
10.8579-0.3773-0.6040.66020.93171.32140.08350.02710.0242-0.1296-0.0514-0.0267-0.10270.016-0.03390.4501-0.0378-0.00830.4349-0.00250.284422.822756.134621.3082
20.05430.2373-0.10641.0949-0.80361.8552-0.0141-0.0653-0.013-0.0393-0.04410.0145-0.00910.03830.05480.38950.03590.00460.5216-0.0010.380434.751121.315516.8059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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