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- PDB-4g3t: Mycobacterium smegmatis DprE1 - hexagonal crystal form -

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Basic information

Entry
Database: PDB / ID: 4g3t
TitleMycobacterium smegmatis DprE1 - hexagonal crystal form
Componentsoxidoreductase DprE1
KeywordsOXIDOREDUCTASE / vao superfamily
Function / homology
Function and homology information


L-gulono-1,4-lactone dehydrogenase activity / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / response to antibiotic / membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / L-gulonolactone/D-arabinono-1,4-lactone oxidase / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.346 Å
AuthorsLi, H. / Jogl, G.
CitationJournal: Proteins / Year: 2013
Title: Crystal structure of decaprenylphosphoryl-beta- D-ribose 2'-epimerase from Mycobacterium smegmatis.
Authors: Li, H. / Jogl, G.
History
DepositionJul 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: oxidoreductase DprE1


Theoretical massNumber of molelcules
Total (without water)44,4411
Polymers44,4411
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.148, 64.148, 275.462
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein oxidoreductase DprE1


Mass: 44441.180 Da / Num. of mol.: 1 / Fragment: UNP residues 66-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC607 / Gene: MSMEG_6382 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star / References: UniProt: A0R607, Oxidoreductases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.68 Å3/Da / Density % sol: 66.59 %
Crystal growTemperature: 277 K / Method: sitting drop / pH: 6.8
Details: 15-20% isopropanol, 0.2 M sodium citrate, 0.5% N,N-dimethyldodecylamine-N-oxide, pH 6.8, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 31, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.346→47.531 Å / Num. all: 28709 / Num. obs: 28628 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 59.372 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 10.74
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.346-2.490.0122.01411714549199.5
2.49-2.660.0123.013937142571100
2.66-2.870.0124.863671139721100
2.87-3.140.0127.723406936941100
3.14-3.510.01212.513076233561100
3.51-4.050.01218.972734830081100
4.05-4.960.01223.632293225681100
4.96-6.970.01223.821762020381100
6.97-47.5310.01224.7389751186195.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1000refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
XDSdata reduction
XDSdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.346→43.239 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.99 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 1288 4.51 %RANDOM
Rwork0.2272 ---
obs0.2286 28559 99.51 %-
all-28559 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.214 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 161.14 Å2 / Biso mean: 69.4773 Å2 / Biso min: 40.33 Å2
Baniso -1Baniso -2Baniso -3
1-11.4955 Å2-0 Å2-0 Å2
2--11.4955 Å2-0 Å2
3----25.5966 Å2
Refinement stepCycle: LAST / Resolution: 2.346→43.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 0 77 2695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032683
X-RAY DIFFRACTIONf_angle_d0.7243641
X-RAY DIFFRACTIONf_chiral_restr0.052400
X-RAY DIFFRACTIONf_plane_restr0.002474
X-RAY DIFFRACTIONf_dihedral_angle_d10.999964
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.346-2.44040.3397910.32393000309199
2.4404-2.55140.34781090.313530113120100
2.5514-2.68590.32671470.276829803127100
2.6859-2.85420.31091460.277529613107100
2.8542-3.07450.3421600.249430023162100
3.0745-3.38380.31481500.266930133163100
3.3838-3.87310.24581560.229930073163100
3.8731-4.87870.18851540.181230963250100
4.8787-43.24590.23951750.20253201337698
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)
10.3989-0.14570.09280.0562-0.07470.58980.102-0.46510.1229-0.00980.1376-0.0139-0.8355-0.42960.00770.54510.18460.00540.8608-0.04550.4729-17.2571-14.623214.0386
20.00230.09760.23640.2431-0.07450.65570.0732-0.0736-0.037-0.1282-0.0068-0.1025-0.3602-0.1308-0.00650.33280.04030.03220.80810.00890.4879-7.057-21.07718.4974
30.4108-0.0011-0.19550.6466-0.06370.08570.0808-0.00940.12730.11210.02180.01370.018-0.58320.1560.2568-0.02960.00281.0336-0.0090.5914-17.0652-24.517137.67
40.4030.4244-0.11840.372-0.33480.29750.084-0.02160.04410.03410.03280.1047-0.2073-0.2590.12670.26490.08710.01480.8267-0.03990.5422-7.5831-20.356435.7082
50.0621-0.04770.1860.0341-0.13740.56780.1524-0.22850.02440.2597-0.2701-0.024-0.5922-0.09330.00170.4427-0.105-0.01920.8712-0.01910.60176.019-15.253140.384
60.8275-0.0776-0.49790.9598-0.44680.6632-0.19060.0336-0.06870.29150.1399-0.3631-0.4290.9674-0.0454-0.0688-0.18430.10511.30970.01970.561210.9941-15.491221.176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ( resid 85 through 129 )A85 - 129
2X-RAY DIFFRACTION2chain 'A' and ( resid 130 through 223 )A130 - 223
3X-RAY DIFFRACTION3chain 'A' and ( resid 224 through 268 )A224 - 268
4X-RAY DIFFRACTION4chain 'A' and ( resid 269 through 389 )A269 - 389
5X-RAY DIFFRACTION5chain 'A' and ( resid 390 through 416 )A390 - 416
6X-RAY DIFFRACTION6chain 'A' and ( resid 417 through 468 )A417 - 468

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