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- PDB-1rqb: Propionibacterium shermanii transcarboxylase 5S subunit -

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Basic information

Entry
Database: PDB / ID: 1rqb
TitlePropionibacterium shermanii transcarboxylase 5S subunit
Componentstranscarboxylase 5S subunit
KeywordsTRANSFERASE / TIM-barrel / carbamylated lysine / transcarboxylase
Function / homology
Function and homology information


methylmalonyl-CoA carboxytransferase / methylmalonyl-CoA carboxytransferase activity / metal ion binding
Similarity search - Function
Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Methylmalonyl-CoA carboxyltransferase 5S subunit
Similarity search - Component
Biological speciesPropionibacterium freudenreichii subsp. shermanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsHall, P.R. / Zheng, R. / Antony, L. / Pusztai-Carey, M. / Carey, P.R. / Yee, V.C.
Citation
Journal: Embo J. / Year: 2004
Title: Transcarboxylase 5S structures: assembly and catalytic mechanism of a multienzyme complex subunit.
Authors: Hall, P.R. / Zheng, R. / Antony, L. / Pusztai-Carey, M. / Carey, P.R. / Yee, V.C.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Expression and crystallization of several forms of the Propionibacterium shermanii transcarboxylase 5S subunit
Authors: Hall, P.R. / Zheng, R. / Pusztai-Carey, M. / van den Akker, F. / Carey, P.R. / Yee, V.C.
History
DepositionDec 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transcarboxylase 5S subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8372
Polymers60,7781
Non-polymers591
Water6,702372
1
A: transcarboxylase 5S subunit
hetero molecules

A: transcarboxylase 5S subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6744
Polymers121,5562
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_754-x+2,y,-z-1/21
Buried area3960 Å2
ΔGint-38 kcal/mol
Surface area35330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.464, 145.938, 79.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-589-

HOH

31A-699-

HOH

41A-791-

HOH

51A-820-

HOH

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Components

#1: Protein transcarboxylase 5S subunit


Mass: 60777.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Propionibacterium freudenreichii subsp. shermanii (bacteria)
Species: Propionibacterium freudenreichii / Strain: subsp. shermanii / Gene: 5S / Plasmid: pETBlue-2 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLacI
References: UniProt: Q70AC7, methylmalonyl-CoA carboxytransferase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 4000, Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0734, 0.9803, 0.9808
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2003
RadiationMonochromator: double flat Si crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07341
20.98031
30.98081
ReflectionResolution: 1.9→50 Å / Num. all: 44245 / Num. obs: 42109 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 6.5 / % possible all: 87

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→33.12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 256613.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1961 4.7 %RANDOM
Rwork0.162 ---
all0.164 44245 --
obs0.164 42109 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.2197 Å2 / ksol: 0.32108 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.61 Å20 Å2
3----0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3663 0 1 372 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it2.373
X-RAY DIFFRACTIONc_mcangle_it3.113.5
X-RAY DIFFRACTIONc_scbond_it4.143.5
X-RAY DIFFRACTIONc_scangle_it5.424
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 278 4.5 %
Rwork0.189 5927 -
obs-6205 85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP2.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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