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- PDB-4fdp: Mycobacterium tuberculosis DprE1 - monoclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 4fdp
TitleMycobacterium tuberculosis DprE1 - monoclinic crystal form
Componentsoxidoreductase DprE1
KeywordsOXIDOREDUCTASE / ALPHA+BETA / decaprenylphosphoryl-beta-D-ribose
Function / homology
Function and homology information


arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / plasma membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / FAD linked oxidase, N-terminal / FAD binding domain / 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
FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / Decaprenylphosphoryl-beta-D-ribose oxidase / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.23 Å
AuthorsBatt, S.M. / Besra, G.S. / Futterer, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by benzothiazinone inhibitors.
Authors: Batt, S.M. / Jabeen, T. / Bhowruth, V. / Quill, L. / Lund, P.A. / Eggeling, L. / Alderwick, L.J. / Futterer, K. / Besra, G.S.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
A: oxidoreductase DprE1
B: oxidoreductase DprE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4235
Polymers104,7832
Non-polymers1,6403
Water3,873215
1
A: oxidoreductase DprE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2463
Polymers52,3911
Non-polymers8552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: oxidoreductase DprE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1772
Polymers52,3911
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.970, 83.620, 81.370
Angle α, β, γ (deg.)90.00, 103.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and resid 7:260 and backbone
211chain 'B' and resid 7:260 and backbone
112chain 'A' and resid 303:314 and backbone
212chain 'B' and resid 303:314 and backbone
113chain 'A' and resid 332:461 and backbone
213chain 'B' and resid 332:461 and backbone

NCS ensembles :
ID
1
2
3

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Components

#1: Protein oxidoreductase DprE1


Mass: 52391.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dprE1, MT3898, Rv3790 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P72056, UniProt: P9WJF1*PLUS, Oxidoreductases
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M imidazole, 34% polypropylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: PILATUS 2M / Detector: PIXEL / Date: Dec 9, 2011
RadiationMonochromator: TOROIDAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.23→83.6 Å / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 14.8
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.3 / Rsym value: 59.4 / % possible all: 97.2

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Processing

Software
NameVersionClassification
GDAdata collection
SHELXDphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.23→78.984 Å / SU ML: 0.33 / σ(F): 1.38 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 2463 5.05 %
Rwork0.1905 --
obs0.1927 48734 98.29 %
all-46277 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.476 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1354 Å20 Å2-10.3381 Å2
2--7.5028 Å20 Å2
3----10.6381 Å2
Refinement stepCycle: LAST / Resolution: 2.23→78.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6362 0 111 215 6688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086623
X-RAY DIFFRACTIONf_angle_d1.1489022
X-RAY DIFFRACTIONf_dihedral_angle_d14.112348
X-RAY DIFFRACTIONf_chiral_restr0.081013
X-RAY DIFFRACTIONf_plane_restr0.0051155
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1016X-RAY DIFFRACTIONPOSITIONAL
12B1016X-RAY DIFFRACTIONPOSITIONAL0.045
21A48X-RAY DIFFRACTIONPOSITIONAL
22B48X-RAY DIFFRACTIONPOSITIONAL0.047
31A520X-RAY DIFFRACTIONPOSITIONAL
32B520X-RAY DIFFRACTIONPOSITIONAL0.063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.27290.31841380.28032478X-RAY DIFFRACTION97
2.2729-2.31930.2931420.26062569X-RAY DIFFRACTION98
2.3193-2.36970.271270.22742531X-RAY DIFFRACTION98
2.3697-2.42490.24821320.22962571X-RAY DIFFRACTION98
2.4249-2.48550.2881300.2232585X-RAY DIFFRACTION98
2.4855-2.55270.30151420.2482561X-RAY DIFFRACTION99
2.5527-2.62780.3311420.22542542X-RAY DIFFRACTION98
2.6278-2.71270.27541240.22262577X-RAY DIFFRACTION98
2.7127-2.80960.26021380.21832579X-RAY DIFFRACTION99
2.8096-2.92210.24351510.21222509X-RAY DIFFRACTION97
2.9221-3.05510.29441400.20572577X-RAY DIFFRACTION99
3.0551-3.21620.29171390.21392607X-RAY DIFFRACTION99
3.2162-3.41770.25611230.21012583X-RAY DIFFRACTION99
3.4177-3.68160.22991420.19492591X-RAY DIFFRACTION98
3.6816-4.05210.21761310.1752571X-RAY DIFFRACTION98
4.0521-4.63830.19511400.14662586X-RAY DIFFRACTION98
4.6383-5.84360.18941450.15442618X-RAY DIFFRACTION99
5.8436-79.03330.18371370.16692636X-RAY DIFFRACTION98

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