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- PDB-1qwg: Crystal structure of Methanococcus jannaschii phosphosulfolactate... -

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Basic information

Entry
Database: PDB / ID: 1qwg
TitleCrystal structure of Methanococcus jannaschii phosphosulfolactate synthase
Components(2R)-phospho-3-sulfolactate synthase
KeywordsLYASE / beta-alpha-barrel
Function / homology
Function and homology information


phosphosulfolactate synthase / phosphosulfolactate synthase activity / coenzyme M biosynthetic process / sulfopyruvate decarboxylase activity
Similarity search - Function
Phosphosulpholactate synthase / (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
Phosphosulfolactate synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsWise, E.L. / Graham, D.E. / White, R.H. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The structural determination of phosphosulfolactate synthase from Methanococcus jannaschii at 1.7-A resolution: an enolase that is not an enolase
Authors: Wise, E.L. / Graham, D.E. / White, R.H. / Rayment, I.
History
DepositionSep 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (2R)-phospho-3-sulfolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6964
Polymers28,4071
Non-polymers2883
Water4,360242
1
A: (2R)-phospho-3-sulfolactate synthase
hetero molecules

A: (2R)-phospho-3-sulfolactate synthase
hetero molecules

A: (2R)-phospho-3-sulfolactate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,08712
Polymers85,2223
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area10140 Å2
ΔGint-210 kcal/mol
Surface area27250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.789, 93.789, 93.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Cell settingcubic
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-473-

HOH

21A-474-

HOH

31A-498-

HOH

41A-499-

HOH

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Components

#1: Protein (2R)-phospho-3-sulfolactate synthase / E.C.4.4.-.- / Phosphosulfolactate synthase / PSL synthase


Mass: 28407.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: ComA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus / References: UniProt: Q57703, Lyases; Carbon-sulfur lyases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.2 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 1.6 M Ammonium sulfate, 100 mM succinate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mM1dropMgCl2
41.6 Mammonium sulfate1reservoir
5100 mMsuccinate1reservoirpH4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→90 Å / Num. all: 29827 / Num. obs: 29827 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.28 / Net I/σ(I): 28.4
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4.7 / % possible all: 56.8
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 31689 / Num. measured all: 446003
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 68.8 %

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→65.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.744 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.094 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19269 1294 5 %RANDOM
Rwork0.17279 ---
obs0.17381 25348 81.8 %-
all-26642 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.062 Å2
Refinement stepCycle: LAST / Resolution: 1.6→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 15 242 2234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222027
X-RAY DIFFRACTIONr_bond_other_d0.0020.021844
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9742726
X-RAY DIFFRACTIONr_angle_other_deg1.46234304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9865250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_nbd_refined0.2150.2441
X-RAY DIFFRACTIONr_nbd_other0.2390.22182
X-RAY DIFFRACTIONr_nbtor_other0.0840.21109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2150
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6651.51237
X-RAY DIFFRACTIONr_mcangle_it1.26121980
X-RAY DIFFRACTIONr_scbond_it2.1023790
X-RAY DIFFRACTIONr_scangle_it3.4884.5746
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.253 32
Rwork0.273 645
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.29

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