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- PDB-4egf: Crystal structure of a L-xylulose reductase from Mycobacterium sm... -

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Basic information

Entry
Database: PDB / ID: 4egf
TitleCrystal structure of a L-xylulose reductase from Mycobacterium smegmatis
ComponentsL-xylulose reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


L-xylulose reductase (NADH) activity / L-xylulose reductase / L-xylulose reductase (NADPH) activity
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-xylulose reductase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Arakaki, T.L. / Staker, B.L. / Fairman, J.W.
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Feb 17, 2016Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-xylulose reductase
B: L-xylulose reductase
C: L-xylulose reductase
D: L-xylulose reductase
E: L-xylulose reductase
F: L-xylulose reductase
G: L-xylulose reductase
H: L-xylulose reductase


Theoretical massNumber of molelcules
Total (without water)217,3368
Polymers217,3368
Non-polymers00
Water15,241846
1
A: L-xylulose reductase
B: L-xylulose reductase
C: L-xylulose reductase
D: L-xylulose reductase


Theoretical massNumber of molelcules
Total (without water)108,6684
Polymers108,6684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-117 kcal/mol
Surface area33510 Å2
MethodPISA
2
E: L-xylulose reductase
F: L-xylulose reductase
G: L-xylulose reductase
H: L-xylulose reductase


Theoretical massNumber of molelcules
Total (without water)108,6684
Polymers108,6684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13250 Å2
ΔGint-124 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.800, 130.750, 114.970
Angle α, β, γ (deg.)90.000, 103.740, 90.000
Int Tables number4
Space group name H-MP1211
Detailstetramer

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Components

#1: Protein
L-xylulose reductase /


Mass: 27166.949 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_3262 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QXD6, L-xylulose reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 18% PEG 6000, 200 mM calcium chloride, PW 28826, MysmA.01365.g.A1.PW28826, pH 8.7, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 93608 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.038 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.360.4612.826198693199.9
2.36-2.420.3973.225546674199.9
2.42-2.490.3453.624856655699.9
2.49-2.570.318423982635899.6
2.57-2.660.2994.323451619199.9
2.66-2.750.2615.122406595799.6
2.75-2.850.2145.821984579799.8
2.85-2.970.1667.521046554399.9
2.97-3.10.1389.120300534099.8
3.1-3.250.11810.419043505199.7
3.25-3.430.08713.518357485799.9
3.43-3.640.06817.217012458099.5
3.64-3.890.05720.615722429398.9
3.89-4.20.0522.714803399299.4
4.2-4.60.04226.513928370199.8
4.6-5.140.04126.8124853346100
5.14-5.940.04823.510844296399.7
5.94-7.270.0426.49482252299.9
7.27-10.290.02340.57443195599.6
10.290.02239.9349493484.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.88 Å
Translation3.5 Å19.88 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.88 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.907 / SU B: 13.544 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4693 5 %RANDOM
Rwork0.187 ---
obs0.19 93608 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.476 Å2
Baniso -1Baniso -2Baniso -3
1-5.48 Å20 Å21.88 Å2
2---1.88 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14426 0 0 846 15272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01914695
X-RAY DIFFRACTIONr_bond_other_d0.0010.029367
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.96820094
X-RAY DIFFRACTIONr_angle_other_deg0.96322902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53552050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32922.738493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.218152059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.68615115
X-RAY DIFFRACTIONr_chiral_restr0.0750.22432
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022897
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 351 -
Rwork0.264 6367 -
all-6718 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.25910.4014-1.17680.9459-0.99092.1760.1909-0.08260.13510.3069-0.03040.1653-0.44690.1295-0.16050.32340.01390.05250.2116-0.04480.2756-17.932412.942343.6531
20.9852-0.97262.5696.24981.33569.5627-0.1475-0.03980.08690.5638-0.10920.1247-0.0173-0.15290.25670.44320.01750.19010.1978-0.11430.2981-18.620920.17350.4556
30.88690.6625-0.83442.2266-1.35431.26280.11590.02870.06040.13830.06540.06250.0281-0.1313-0.18130.3097-0.01050.03340.26470.01190.2714-26.52754.13848.3145
40.19030.0591-0.1990.7740.00840.24550.03140.05970.01350.2875-0.05770.182-0.03720.01060.02630.2874-0.02810.03040.2701-0.00430.268-14.837-5.215442.7837
51.20250.11680.24230.41260.21720.53320.04320.06960.00530.1143-0.01490.01440.0120.0557-0.02820.2923-0.0111-0.01720.26620.00450.2441-3.57592.614736.6027
61.75610.6131-0.75450.71280.33631.9151-0.0904-0.0403-0.02340.0138-0.00470.00510.22840.28090.0950.25270.02780.0080.2785-0.01960.26457.5807-36.148914.2192
72.44540.1278-0.99637.0626-3.80184.06710.03260.398-0.1981-0.041-0.1569-0.23390.19110.54610.12430.23140.0360.03030.3045-0.03720.203611.4476-35.89616.9265
80.18070.0872-0.17431.0940.17010.3361-0.01650.0267-0.0218-0.1046-0.0037-0.0938-0.0105-0.03230.02020.23570.0015-0.00780.2881-0.01280.25912.7338-19.671612.6162
94.3455-2.9421-7.78987.97474.330614.21710.3925-0.270.5934-0.2630.4528-1.1166-0.8440.5965-0.84540.1888-0.1137-0.10770.45720.03360.340617.807-17.45230.7646
100.6768-0.2580.21430.80670.27030.25350.0355-0.02910.02180.0656-0.0378-0.05040.0935-0.00760.00230.2581-0.0077-0.00220.28990.00350.26721.2646-26.106527.4885
112.4161-0.8523-1.58711.4751.19052.0783-0.11060.0508-0.16890.04840.09970.14090.2927-0.00590.01090.3748-0.01840.03280.19710.02560.2239-9.5749-40.253838.3053
123.0888-0.06383.17380.027-0.568113.5201-1.0003-1.0063-0.8448-0.0120.1556-0.063-0.6747-1.65120.84470.55870.19160.38340.48960.16550.4879-21.2343-42.31847.5676
132.54670.2974-2.24793.19293.49396.4705-0.0570.23950.04080.2351-0.11570.24820.3366-0.42080.17270.4436-0.04210.08420.14830.15470.3647-15.8196-40.654948.4099
140.2956-0.5199-0.13011.3358-0.10350.4238-0.04880.0386-0.0670.2403-0.01490.18550.03410.02530.06370.3384-0.030.05360.23330.00680.2418-13.3726-22.952243.1278
151.21270.1077-0.14730.731-0.33461.38-0.02310.10840.00640.16260.04390.23980.0601-0.1883-0.02080.2515-0.01840.03660.2577-0.00550.303-16.0252-27.480626.8347
161.2236-0.0071-1.34411.20931.15633.78170.11950.10520.14430.0202-0.00390.0439-0.199-0.1896-0.11560.28910.0254-0.00890.24740.05360.2516-5.235816.817616.8078
171.80150.1854-1.5930.9444-2.16375.75990.28770.13080.0857-0.1350.03820.1053-0.0117-0.1865-0.32590.4854-0.0612-0.00150.13830.07850.2285-0.943917.39854.6603
180.08030.0699-0.01221.30070.23110.32980.03130.00460.0373-0.1397-0.0094-0.0513-0.0657-0.0033-0.02190.2492-0.0007-0.00780.29340.01280.24850.77030.130813.8356
1913.93275.1002-9.060811.8468-4.43916.0205-1.58611.8401-1.2712-2.33840.87270.5691.2185-1.19790.71340.5813-0.3473-0.05750.5449-0.12870.2277-22.0348-3.50029.1737
201.53990.1689-0.1080.65560.30880.85130.04370.06420.0255-0.1382-0.043-0.0178-0.0451-0.1475-0.00070.2280.0231-0.01850.29130.02010.2613-12.28823.656323.2021
212.07110.15490.13130.96870.95941.03180.05170.0034-0.07450.0254-0.0770.04830.1677-0.15840.02530.3154-0.05060.00420.24820.01930.22764.059-32.223796.8014
222.0547-0.1601-1.81351.2211.34422.82340.12230.06160.07310.0992-0.21360.14210.023-0.18540.09130.3128-0.02170.01490.25610.02090.2305-2.8304-30.186105.5505
230.05020.014-0.13871.2153-0.21060.45480.03620.0172-0.00810.1886-0.05670.0877-0.05120.0390.02050.2703-0.02940.00720.27430.00270.2446.3804-15.107399.8973
244.31182.2625-6.09395.2975-6.444911.21310.26390.03690.3210.19790.50380.6277-0.5093-0.4976-0.76780.2740.0841-0.04740.35090.03810.2952-8.9189-14.073281.5076
250.30260.1510.01530.6954-0.2780.53890.03720.02920.0313-0.0462-0.05420.02980.0865-0.0190.0170.27080.0052-0.02390.2651-0.0010.27257.3424-22.917685.6081
261.1112-0.0751-0.4711.83410.92632.0641-0.00380.07830.1408-0.20930.1038-0.0241-0.2865-0.062-0.09990.2922-0.01690.00190.25730.02160.240327.566415.057268.272
271.0757-2.2826-1.307517.38816.85995.84720.14930.03130.1167-0.6266-0.00460.0335-0.0781-0.3735-0.14470.3751-0.05240.00560.2410.0450.156328.121916.470655.1837
280.9254-1.2822-0.273.0778-0.72641.1511-0.04570.02470.1289-0.2430.0173-0.29940.13480.12220.02830.3149-0.08970.08960.2921-0.03150.22536.44914.829258.9519
290.9071.23220.10091.71970.14690.1457-0.22340.0591-0.0402-0.40080.1188-0.1013-0.03260.06550.10450.34170.00260.01230.2603-0.02430.260924.7943-3.09762.0709
300.2027-0.15-0.13970.5928-0.1520.3459-0.0346-0.07690.0315-0.1554-0.0111-0.04950.0187-0.00720.04570.26560.0063-0.00110.27470.00520.257420.69010.178171.4162
310.7338-0.248-0.99590.9686-0.04461.9588-0.0062-0.00890.16820.10410.02640.0199-0.21220.1544-0.02020.2814-0.0298-0.00190.2499-0.02040.283315.694820.72691.8607
321.35221.35930.18222.7172.35433.62240.3053-0.04590.17310.5038-0.14390.12370.132-0.0036-0.16140.4378-0.05710.05450.1999-0.06240.25699.525721.1555103.9393
330.09120.245-0.11371.2943-0.10880.22210.05720.00880.02430.1907-0.07820.0531-0.0287-0.00930.02110.2588-0.0120.00180.2859-0.02270.26419.39533.811196.4723
3410.6401-4.3015-4.137415.715812.432911.8831-0.5795-1.326-0.57151.75640.7209-0.34230.90420.8209-0.14140.40420.0241-0.07560.480.16920.093131.78611.3676101.3841
351.5207-0.2412-0.19740.1599-0.00150.7632-0.0554-0.10140.00980.04740.00590.0078-0.01260.0980.04950.2387-0.0202-0.01570.2959-0.00090.255921.98366.684387.0032
361.36590.1857-1.52112.0547-0.29021.7015-0.2078-0.121-0.0613-0.03010.1482-0.08480.26620.12790.05960.33320.0225-0.0070.2179-0.00140.250517.6154-38.378276.3488
371.017-1.90210.35454.5399-0.46982.7362-0.0888-0.03050.0189-0.46820.1677-0.56120.24420.0848-0.07890.4920.00530.2370.1568-0.11640.380924.5156-38.707864.4481
380.14890.2572-0.11310.7142-0.01830.4056-0.0236-0.0642-0.0427-0.1791-0.0213-0.15570.0402-0.01380.04490.31560.02680.04470.23520.01280.264622.5084-20.79571.1026
390.8559-1.4629-3.20892.53255.565112.24370.231-0.17960.2375-0.26870.4896-0.3906-0.56660.9938-0.72060.08570.09660.14770.5557-0.01080.610837.434-22.757188.4656
400.42380.144-0.44840.5174-0.02610.77250.0564-0.11960.0397-0.0631-0.1249-0.1170.1177-0.01480.06850.28610.00010.00470.27460.00610.271418.8558-25.343285.465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 53
2X-RAY DIFFRACTION2A54 - 67
3X-RAY DIFFRACTION3A68 - 103
4X-RAY DIFFRACTION4A104 - 208
5X-RAY DIFFRACTION5A209 - 262
6X-RAY DIFFRACTION6B6 - 56
7X-RAY DIFFRACTION7B57 - 79
8X-RAY DIFFRACTION8B80 - 202
9X-RAY DIFFRACTION9B203 - 221
10X-RAY DIFFRACTION10B222 - 262
11X-RAY DIFFRACTION11C6 - 44
12X-RAY DIFFRACTION12C45 - 60
13X-RAY DIFFRACTION13C61 - 78
14X-RAY DIFFRACTION14C79 - 200
15X-RAY DIFFRACTION15C201 - 262
16X-RAY DIFFRACTION16D6 - 46
17X-RAY DIFFRACTION17D47 - 79
18X-RAY DIFFRACTION18D80 - 201
19X-RAY DIFFRACTION19D202 - 221
20X-RAY DIFFRACTION20D222 - 262
21X-RAY DIFFRACTION21E6 - 33
22X-RAY DIFFRACTION22E34 - 79
23X-RAY DIFFRACTION23E80 - 202
24X-RAY DIFFRACTION24E203 - 221
25X-RAY DIFFRACTION25E222 - 262
26X-RAY DIFFRACTION26F6 - 47
27X-RAY DIFFRACTION27F48 - 64
28X-RAY DIFFRACTION28F65 - 89
29X-RAY DIFFRACTION29F90 - 116
30X-RAY DIFFRACTION30F117 - 262
31X-RAY DIFFRACTION31G6 - 44
32X-RAY DIFFRACTION32G45 - 86
33X-RAY DIFFRACTION33G87 - 200
34X-RAY DIFFRACTION34G201 - 221
35X-RAY DIFFRACTION35G222 - 262
36X-RAY DIFFRACTION36H6 - 43
37X-RAY DIFFRACTION37H44 - 90
38X-RAY DIFFRACTION38H91 - 202
39X-RAY DIFFRACTION39H203 - 221
40X-RAY DIFFRACTION40H222 - 262

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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