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- PDB-4u5r: Crystal structure of D106A mutant of RhCC (YP_702633.1) from Rhod... -

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Basic information

Entry
Database: PDB / ID: 4u5r
TitleCrystal structure of D106A mutant of RhCC (YP_702633.1) from Rhodococcus jostii RHA1 at 1.55 Angstrom
ComponentsRhCC
KeywordsISOMERASE / beta-alpha-beta structural motif / magnesium binding enzyme / tautomerase superfamily
Function / homologyTautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / metal ion binding / Alpha Beta / Tautomerase cis-CaaD-like domain-containing protein
Function and homology information
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPoddar, H. / Rozeboom, H.J. / Thunnissen, A.M.W.H.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchVIDI grant 700.56.421 Netherlands
European Research Coucil242293
CitationJournal: Biochemistry / Year: 2015
Title: Functional and structural characterization of an unusual cofactor-independent oxygenase.
Authors: Baas, B.J. / Poddar, H. / Geertsema, E.M. / Rozeboom, H.J. / de Vries, M.P. / Permentier, H.P. / Thunnissen, A.M. / Poelarends, G.J.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RhCC
B: RhCC
C: RhCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0464
Polymers52,9243
Non-polymers1221
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-16 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.795, 57.784, 92.026
Angle α, β, γ (deg.)90.0, 90.41, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11B-236-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein RhCC


Mass: 17641.174 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: C-terminal His6-tagged / Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Gene: RHA1_ro02670 / Plasmid: pET-20b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0SDB1
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Halogens, 100mM Tris Bicine, 30% PEGMME 550 PEG 20000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→188.45 Å / Num. all: 74309 / Num. obs: 74309 / % possible obs: 97.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 14.86 Å2 / Rpim(I) all: 0.057 / Rrim(I) all: 0.101 / Rsym value: 0.084 / Net I/av σ(I): 5.08 / Net I/σ(I): 7.4 / Num. measured all: 197991
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.55-1.632.40.255323982101930.1890.2553.592
1.63-1.732.60.1844.226795103020.130.1844.398.1
1.73-1.852.60.1395.42567797050.0970.1395.498.2
1.85-22.70.0997.32431890650.0680.0997.298.5
2-2.192.70.0858.42255183140.0580.0858.898.6
2.19-2.452.70.0798.82083875850.0540.0799.898.9
2.45-2.832.80.0768.91865467380.0520.07610.499.4
2.83-3.462.80.0798.31595456960.0540.07910.899.3
3.46-4.92.90.0749.11253643870.050.07411.398
4.9-50.0062.90.0826.9668623240.0540.08211.393

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U5P

4u5p


Resolution: 1.55→43.994 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1749 3832 5.02 %
Rwork0.1597 72530 -
obs0.1605 74309 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.91 Å2 / Biso mean: 19.446 Å2 / Biso min: 7.2 Å2
Refinement stepCycle: LAST / Resolution: 1.55→43.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 8 465 4178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5402-1.55970.1316930.11971620171359
1.5597-1.58020.17531340.136426332767100
1.5802-1.60190.12231650.102827562921100
1.6019-1.62480.12121020.102727182820100
1.6248-1.6490.1431510.111727412892100
1.649-1.67480.17461220.11126902812100
1.6748-1.70220.12731680.11327222890100
1.7022-1.73160.15491240.11427102834100
1.7316-1.76310.14711700.11827002870100
1.7631-1.7970.14651280.123427352863100
1.797-1.83370.14341340.143327182852100
1.8337-1.87360.1941400.155227342874100
1.8736-1.91710.18181630.147327132876100
1.9171-1.96510.161590.145726752834100
1.9651-2.01820.1791410.15527182859100
2.0182-2.07760.20861340.167427532887100
2.0776-2.14470.18741150.167127652880100
2.1447-2.22130.171260.169727532879100
2.2213-2.31020.20781520.183727372889100
2.3102-2.41540.20821450.184927152860100
2.4154-2.54270.1911260.180427152841100
2.5427-2.7020.19691610.178927312892100
2.702-2.91060.19161160.184327562872100
2.9106-3.20340.1912340.17126832917100
3.2034-3.66670.16221480.165527372885100
3.6667-4.61890.12921310.141927702901100
4.6189-44.01210.19831500.18122832298299

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