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- PDB-4g3u: Mycobacterium smegmatis DprE1 - monoclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 4g3u
TitleMycobacterium smegmatis DprE1 - monoclinic crystal form
Componentsoxidoreductase DprE1
KeywordsOXIDOREDUCTASE / vao superfamily
Function / homology
Function and homology information


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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.689 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: oxidoreductase DprE1
B: oxidoreductase DprE1


Theoretical massNumber of molelcules
Total (without water)88,8822
Polymers88,8822
Non-polymers00
Water5,170287
1
A: oxidoreductase DprE1


Theoretical massNumber of molelcules
Total (without water)44,4411
Polymers44,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: oxidoreductase DprE1


Theoretical massNumber of molelcules
Total (without water)44,4411
Polymers44,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.152, 65.808, 108.504
Angle α, β, γ (deg.)90.000, 109.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 86:274 or resseq 308:322 or resseq 338:468 )
21chain B and (resseq 86:274 or resseq 308:322 or resseq 338:468 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPHEPHEchain 'A' and (resseq 86:274 or resseq 308:322 or resseq 338:468 )AA86 - 27421 - 209
12GLYGLYHISHISchain 'A' and (resseq 86:274 or resseq 308:322 or resseq 338:468 )AA308 - 322243 - 257
13GLYGLYLEULEUchain 'A' and (resseq 86:274 or resseq 308:322 or resseq 338:468 )AA338 - 468273 - 403
21ARGARGPHEPHEchain 'B' and (resseq 86:274 or resseq 308:322 or resseq 338:468 )BB86 - 27421 - 209
22GLYGLYHISHISchain 'B' and (resseq 86:274 or resseq 308:322 or resseq 338:468 )BB308 - 322243 - 257
23GLYGLYLEULEUchain 'B' and (resseq 86:274 or resseq 308:322 or resseq 338:468 )BB338 - 468273 - 403

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Components

#1: Protein oxidoreductase DprE1


Mass: 44441.180 Da / Num. of mol.: 2 / 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.: 287 / 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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 277 K / Method: sitting drop / pH: 7.5
Details: 30% butanol, 0.2 M sodium chloride, 0.1 M Tris, 0.5% N,N-dimethyldodecylamine-N-oxide, pH 7.5, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2010
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.689→102.589 Å / Num. all: 39473 / Num. obs: 36583 / % possible obs: 92.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 45.658 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.689-2.850.6252.34180625862192.6
2.85-3.050.4023.42177585627195.2
3.05-3.290.2455.44167805283194.6
3.29-3.60.1717.06151494760194
3.6-4.020.10810.9136594302192.7
4.02-4.640.06219.74121143771192
4.64-5.670.05521.3102693153190.6
5.67-7.960.05122.6479522436189
7.96-102.5890.02241.3644151389185.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1000refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.689→34.196 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.99 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 1838 5.03 %RANDOM
Rwork0.2201 ---
obs0.2218 36552 92.79 %-
all-36552 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.978 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 181.62 Å2 / Biso mean: 46.7215 Å2 / Biso min: 5.98 Å2
Baniso -1Baniso -2Baniso -3
1-3.6729 Å20 Å27.2874 Å2
2---6.1284 Å20 Å2
3---7.6137 Å2
Refinement stepCycle: LAST / Resolution: 2.689→34.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5370 0 0 287 5657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035502
X-RAY DIFFRACTIONf_angle_d0.7157468
X-RAY DIFFRACTIONf_chiral_restr0.049824
X-RAY DIFFRACTIONf_plane_restr0.003972
X-RAY DIFFRACTIONf_dihedral_angle_d12.2471978
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2610X-RAY DIFFRACTIONPOSITIONAL0.011
12B2610X-RAY DIFFRACTIONPOSITIONAL0.011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.689-2.76180.3661360.32082587272389
2.7618-2.8430.37291310.28192719285096
2.843-2.93470.30841330.26862703283695
2.9347-3.03950.28741630.25862715287895
3.0395-3.16120.29081420.2442728287095
3.1612-3.30490.30121390.22972705284495
3.3049-3.4790.29781560.23552681283794
3.479-3.69670.30771310.26692685281693
3.6967-3.98180.24981420.21392656279893
3.9818-4.38170.1931270.17022686281392
4.3817-5.01410.1581490.15922636278592
5.0141-6.31070.22311290.19622615274490
6.3107-34.19920.22971600.20412598275888
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)
10.00490.00210.00280.00670.00710.0048-0.01420.04210.0089-0.0033-0.00850.0111-0.033-0.0103-0.00510.1245-0.0457-0.03960.1308-0.08950.0764-13.9657-7.4717-5.4227
20.00320.00110.0020.0024-0.0009-0.001-0.0020.0157-0.0079-0.0185-0.01070.0206-0.009-0.0184-0-0.0424-0.01-0.09480.1408-0.03130.2056-26.6859-3.3772-2.6647
30.0174-0.0119-0.0150.0162-0.00620.03560.02890.00710.0201-0.0158-0.00220.1227-0.08140.10510.0259-0.39060.1083-0.06050.09130.01180.3581-35.1237-1.9111-0.7804
40.00330.00040.00120.0003-0.00240.00130.0410.00750.0126-0.04470.02830.001-0.01690.0035-00.158-0.0015-0.0560.18650.00750.3899-42.991514.6432-9.3889
50.0013-0.0032-0.0020.010.00490.0032-0.0324-0.00690.0201-0.0014-0.04710.0485-0.04040.0464-0.01430.0838-0.0083-0.04820.17640.06130.2293-23.708718.4019-3.6258
60.00340.0030.00350.0165-0.00190.00270.0171-0.0215-0.01620.01270.0125-0.0256-0.01990.02770.00670.16090.0194-0.010.1578-0.01780.05240.0028-11.889316.6156
70.00220.0053-0.00490.0126-0.00880.00740.0229-0.02870.00750.02830.032-0.01560.0028-0.01530.00430.4334-0.00610.04550.2387-0.02030.0566-6.6713-16.230727.7042
80.088-0.0127-0.00670.01450.03490.03120.0103-0.03870.03340.4004-0.0017-0.0127-0.1203-0.0305-0.02580.2944-0.00730.26670.10660.0364-0.5011-11.1493-17.885835.0608
90.0003-0.0015-0.00120.00040.00050.0056-0.0309-0.0088-0.04170.0203-0.0228-0.03900.000400.59670.02260.13710.33380.03560.3111-5.9086-35.016544.5014
100.0054-0.0013-0.00520.00240.00070.00880.0068-0.0016-0.01240.0569-0.02140.01660.0285-0.0159-0.00460.2830.0530.02950.14280.02820.0273-5.4459-37.920624.2371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ( resid 75 through 115 )A75 - 115
2X-RAY DIFFRACTION2chain 'A' and ( resid 116 through 148 )A116 - 148
3X-RAY DIFFRACTION3chain 'A' and ( resid 149 through 389 )A149 - 389
4X-RAY DIFFRACTION4chain 'A' and ( resid 390 through 417 )A390 - 417
5X-RAY DIFFRACTION5chain 'A' and ( resid 418 through 468 )A418 - 468
6X-RAY DIFFRACTION6chain 'B' and ( resid 75 through 115 )B75 - 115
7X-RAY DIFFRACTION7chain 'B' and ( resid 116 through 148 )B116 - 148
8X-RAY DIFFRACTION8chain 'B' and ( resid 149 through 389 )B149 - 389
9X-RAY DIFFRACTION9chain 'B' and ( resid 390 through 417 )B390 - 417
10X-RAY DIFFRACTION10chain 'B' and ( resid 418 through 468 )B418 - 468

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