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- PDB-4psu: Crystal structure of alpha/beta hydrolase from Rhodopseudomonas p... -

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Basic information

Entry
Database: PDB / ID: 4psu
TitleCrystal structure of alpha/beta hydrolase from Rhodopseudomonas palustris CGA009
ComponentsAlpha/beta hydrolaseAlpha/beta hydrolase superfamily
KeywordsHYDROLASE / alpha/beta hydrolase / esterase
Function / homology
Function and homology information


Putative magnesium chelatase accessory protein / Alpha/beta hydrolase family / 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
Alpha/beta hydrolase fold
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsNocek, B. / Hajighasemi, M. / Xu, X. / Cui, H. / Savchenko, A. / Yakunin, A.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of alpha/beta hydrolase from Rhodopseudomonas palustris CGA009
Authors: Nocek, B. / Hajighasemi, M. / Xu, X. / Cui, H. / Savchenko, A. / Yakunin, A.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7282
Polymers32,1811
Non-polymers5471
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.013, 87.425, 93.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Alpha/beta hydrolase / Alpha/beta hydrolase superfamily


Mass: 32181.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA1511 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N9M9, Hydrolases
#2: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M potassium thiocyanate, 20% PEG3350, 4% Jeffmine M-600, 1/300 trypsin, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2013 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→32 Å / Num. all: 16900 / Num. obs: 16885 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.24 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
CCP4model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→31.961 Å / SU ML: 0.25 / σ(F): 2 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 734 5.14 %RANDOM
Rwork0.1806 ---
all0.184 ---
obs0.1827 14607 88.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→31.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 22 69 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042230
X-RAY DIFFRACTIONf_angle_d0.8463036
X-RAY DIFFRACTIONf_dihedral_angle_d14.562811
X-RAY DIFFRACTIONf_chiral_restr0.032342
X-RAY DIFFRACTIONf_plane_restr0.005391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28780.3061700.23041197X-RAY DIFFRACTION35
2.2878-2.39190.2821800.22961606X-RAY DIFFRACTION48
2.3919-2.5180.20821260.22552108X-RAY DIFFRACTION61
2.518-2.67560.31091150.22742688X-RAY DIFFRACTION79
2.6756-2.88210.30621790.22913133X-RAY DIFFRACTION93
2.8821-3.17190.27772160.20953321X-RAY DIFFRACTION99
3.1719-3.63030.21171810.17583396X-RAY DIFFRACTION99
3.6303-4.57170.18571650.14053348X-RAY DIFFRACTION99
4.5717-31.96470.16521720.16043267X-RAY DIFFRACTION95
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)
10.948-0.20090.03811.4107-0.32170.94810.00370.12340.3222-0.07520.05890.22490.031-0.1027-0.13090.1812-0.01290.00440.17680.08730.243820.7117.938472.204
20.5079-0.1797-0.53460.21960.31150.6707-0.2014-0.0185-0.214-0.2038-0.03260.3230.1030.1283-0.21120.2068-0.00910.01480.16680.01110.24615.83351.043477.0525
30.1617-0.1518-0.08520.15550.03660.1905-0.0477-0.31760.17040.31860.11350.03910.14780.028600.32440.06310.03720.4076-0.070.294618.896214.449192.2976
41.2303-0.17060.27281.6538-0.27940.8717-0.08550.0145-0.0555-0.15350.02840.01160.2240.1077-0.00430.2413-0.03410.01070.18760.00590.226526.53280.486873.9388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 127 )
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 292 )

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