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- PDB-1u83: PSL synthase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1u83
TitlePSL synthase from Bacillus subtilis
ComponentsPhosphosulfolactate synthase
KeywordsLYASE / Bacillus subtilis / structural genomics / Phosphosulfolactate synthase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphosulfolactate synthase / phosphosulfolactate synthase activity
Similarity search - Function
(2R)-phospho-3-sulpholactate synthase, ComA / (2R)-phospho-3-sulpholactate synthase, ComA superfamily / (2R)-phospho-3-sulfolactate synthase (ComA) / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphosulfolactate synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsCuff, M.E. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: PSL synthase from Bacillus subtilis
Authors: Cuff, M.E. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 26, 2012Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphosulfolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7516
Polymers31,2851
Non-polymers4665
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphosulfolactate synthase
hetero molecules

A: Phosphosulfolactate synthase
hetero molecules

A: Phosphosulfolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,25418
Polymers93,8563
Non-polymers1,39915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area10490 Å2
ΔGint-85 kcal/mol
Surface area26680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.071, 92.071, 92.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1132-

HOH

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Components

#1: Protein Phosphosulfolactate synthase / / (2R)-phospho-3-sulfolactate synthase / PSL synthase


Mass: 31285.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: comA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O06739, phosphosulfolactate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: Ammonium phosphate, Bis-Tris, ethylene glycol, glycerol, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945, 0.97921
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 29, 2004 / Details: SBC2
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979211
ReflectionResolution: 2.2→46.04 Å / Num. all: 13466 / Num. obs: 13466 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 32.3 Å2 / Limit h max: 41 / Limit h min: 2 / Limit k max: 29 / Limit k min: 2 / Limit l max: 29 / Limit l min: 0 / Observed criterion F max: 1977281.07 / Observed criterion F min: 10 / Rsym value: 0.055 / Net I/σ(I): 12.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.17 / Rsym value: 0.563 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-2000data reduction
SHELXDphasing
MLPHAREphasing
DMmodel building
CNS1.1refinement
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→46.04 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 671 5 %RANDOM
Rwork0.188 ---
all0.1922 13490 --
obs0.1922 13466 99.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 66.7705 Å2 / ksol: 0.385885 e/Å3
Displacement parametersBiso max: 91.4 Å2 / Biso mean: 40.73 Å2 / Biso min: 20.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 2.2→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 28 176 2013
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg22.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.75
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.2-2.30.266704.20.22915910.0321702166197.6
2.3-2.420.228834.90.20715980.0251686168199.7
2.42-2.570.231804.90.20715580.0261640163899.9
2.57-2.770.247885.30.19315750.0261665166399.9
2.77-3.050.23845.10.19515760.0251661166099.9
3.05-3.490.229774.60.17816130.02616901690100
3.49-4.40.2298650.16616170.02517031703100
4.4-46.040.1911035.80.19616670.0191771177099.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.paramgol.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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