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- PDB-3u7i: The crystal structure of FMN-dependent NADH-azoreductase 1 (GBAA0... -

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Basic information

Entry
Database: PDB / ID: 3u7i
TitleThe crystal structure of FMN-dependent NADH-azoreductase 1 (GBAA0966) from Bacillus anthracis str. Ames Ancestor
ComponentsFMN-dependent NADH-azoreductase 1
KeywordsOXIDOREDUCTASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


FMN-dependent NADH-azoreductase / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on NAD(P)H as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / : / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / FMN-dependent NADH:quinone oxidoreductase 1
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsZhang, R. / Gu, M. / Tan, K. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of FMN-dependent NADH-azoreductase 1 (GBAA0966) from Bacillus anthracis str. Ames Ancestor
Authors: Zhang, R. / Gu, M. / Tan, K. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Data collection
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: FMN-dependent NADH-azoreductase 1
B: FMN-dependent NADH-azoreductase 1
C: FMN-dependent NADH-azoreductase 1
D: FMN-dependent NADH-azoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,71216
Polymers103,9894
Non-polymers72312
Water15,853880
1
A: FMN-dependent NADH-azoreductase 1
C: FMN-dependent NADH-azoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3918
Polymers51,9952
Non-polymers3976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-60 kcal/mol
Surface area20560 Å2
MethodPISA
2
B: FMN-dependent NADH-azoreductase 1
D: FMN-dependent NADH-azoreductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3218
Polymers51,9952
Non-polymers3266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-57 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.802, 113.470, 91.115
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
FMN-dependent NADH-azoreductase 1 / Azo-dye reductase 1 / FMN-dependent NADH-azo compound oxidoreductase 1


Mass: 25997.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor
Gene: azoR1, Bacillus anthracis, BAS0908, BA_0966, GBAA_0966
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): ML21(DE3)majic
References: UniProt: Q81UB2, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16M MgCl, 0.08M Tris, 24% PEG4000, 20% Glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.223
ReflectionResolution: 1.75→31 Å / Num. all: 105368 / Num. obs: 105368 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 17
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→30.916 Å / σ(F): 1.35 / Phase error: 23.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1795 5261 5.03 %
Rwork0.1511 --
obs0.1524 104646 99.64 %
all-104643 -
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.735 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5385 Å2-0 Å22.3669 Å2
2---3.7341 Å2-0 Å2
3---6.2726 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7091 0 38 880 8009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077306
X-RAY DIFFRACTIONf_angle_d0.9259878
X-RAY DIFFRACTIONf_dihedral_angle_d13.2542757
X-RAY DIFFRACTIONf_chiral_restr0.0671115
X-RAY DIFFRACTIONf_plane_restr0.0031257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78020.25922700.2344949X-RAY DIFFRACTION94
1.7802-1.81250.2432600.22024892X-RAY DIFFRACTION94
1.8125-1.84740.23212240.21414953X-RAY DIFFRACTION95
1.8474-1.88510.22782740.20564948X-RAY DIFFRACTION94
1.8851-1.92610.20652480.19534920X-RAY DIFFRACTION95
1.9261-1.97090.21582450.18774958X-RAY DIFFRACTION95
1.9709-2.02020.2132520.18895022X-RAY DIFFRACTION95
2.0202-2.07480.20382610.18324931X-RAY DIFFRACTION95
2.0748-2.13580.18712780.17474934X-RAY DIFFRACTION94
2.1358-2.20470.19692690.17754970X-RAY DIFFRACTION95
2.2047-2.28350.21272320.16575003X-RAY DIFFRACTION96
2.2835-2.37490.18212450.16645013X-RAY DIFFRACTION95
2.3749-2.48290.20772530.16164979X-RAY DIFFRACTION95
2.4829-2.61370.18322720.15944952X-RAY DIFFRACTION95
2.6137-2.77740.19482650.15555021X-RAY DIFFRACTION95
2.7774-2.99160.18672820.1484967X-RAY DIFFRACTION95
2.9916-3.29230.17542660.13254992X-RAY DIFFRACTION95
3.2923-3.76790.1432830.11214971X-RAY DIFFRACTION95
3.7679-4.74390.1232720.09715029X-RAY DIFFRACTION95
4.7439-29.28510.18512770.1475008X-RAY DIFFRACTION94
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)
11.6553-1.01650.42121.56020.38881.25270.1453-0.3349-0.22950.1485-0.06710.1050.115-0.0144-0.03740.1523-0.0009-0.03620.10980.04510.077438.309269.978421.92
26.811-0.4436-0.16511.81520.20661.4333-0.1-0.1647-0.5021-0.00540.0654-0.00170.20240.0263-0.06460.25820.0037-0.06050.09160.00220.120440.394361.562517.2848
32.0371-0.7589-0.083920.23591.0308-0.0594-0.173-0.06160.1810.0943-0.02470.0450.0245-0.03850.1589-0.0083-0.04180.14860.01930.113140.528475.8124.45
46.5414.1706-0.62134.46451.26778.3391-0.1302-0.00861.06040.39330.0457-0.2331-0.91940.38930.02660.26750.002-0.10050.1571-0.07610.457637.3108100.129129.1447
54.3375-2.075-1.48837.56913.29174.7347-0.0523-0.49670.32150.45590.1529-0.1873-0.1559-0.0142-0.12490.15640.022-0.06920.1476-0.0320.137841.954887.697628.6045
61.2631-0.39940.39110.3385-0.05210.5421-0.02040.03210.0881-0.06650.02580.01970.0328-0.01510.0030.14540.0094-0.01170.1280.02870.110433.107278.504716.8833
73.87880.4277-1.1695.8025-1.63845.59210.05810.52530.9004-0.5982-0.1235-0.0824-1.07410.07620.01220.3594-0.0025-0.05250.1780.13120.38243.22594.801512.1879
82.0532-0.18970.59290.6431-0.23081.11090.07490.21510.0144-0.2133-0.0669-0.060.02180.0067-0.00060.18680.0406-0.01590.15170.03120.081933.738977.5366.9344
92.91370.21181.06413.22260.57711.61090.03780.341-0.205-0.3402-0.00090.01730.1237-0.035-0.03920.17460.056-0.04180.15820.00130.080832.531368.54087.0658
105.5281-0.3765-2.12711.59650.01871.1322-0.10410.2975-0.5077-0.23960.02590.06620.1795-0.03110.1290.30450.0442-0.060.143-0.03260.13240.687159.14668.1775
112.26240.1281-0.90111.43780.03211.87320.0073-0.13040.6268-0.05010.14330.1369-0.1749-0.0973-0.07470.10280.0144-0.03350.0770.01470.150713.2715103.04665.6492
122.1105-0.0153-1.46961.1536-0.1352.4180.0448-0.05560.6040.0930.06650.1836-0.245-0.0096-0.05890.24570.0082-0.01770.10120.02720.181612.9561110.302360.5639
131.26430.28230.44983.0225-0.23872.3577-0.1109-0.20270.11380.15290.23630.1095-0.2024-0.13-0.08990.0944-0.00160.0080.12060.00190.081714.089197.611169.5728
143.4664-1.60820.47231.36060.80577.9871-0.2111-0.1667-0.61860.1541-0.00230.18871.5914-0.64370.09180.432-0.07450.01120.22120.01380.131218.470374.364877.5999
151.03650.0937-0.44261.5847-0.71781.28960.0194-0.1392-0.0460.04460.05710.13330.0453-0.0105-0.08050.1019-0.0017-0.03770.12630.00870.080617.391690.391167.9663
168.26281.56772.54297.07612.93322.2769-0.12740.5392-1.0903-0.40820.08420.1241.2824-0.2080.02420.4996-0.0741-0.01930.213-0.01490.29779.428976.76261.3464
172.00420.0057-0.37411.899-0.39671.79880.04130.18310.0556-0.2942-0.00880.06670.1168-0.0319-0.03360.17280.0187-0.05130.1510.01580.088818.041194.974351.3322
183.9437-0.83630.9930.53290.18580.80260.08840.07560.2749-0.1581-0.0607-0.0618-0.2701-0.0518-0.04670.26570.04230.00560.15290.07760.181110.9797111.356251.4797
190.8089-0.5246-0.40821.6605-0.78191.0441-0.0097-0.07140.79270.1761-0.0432-0.1159-0.26290.04830.06840.17510.0048-0.01120.1015-0.04570.367413.5547100.721718.5913
202.8427-1.03530.46612.2703-0.17491.0385-0.011-0.4253-0.43740.25270.08110.25120.2117-0.0812-0.0770.144-0.00690.01390.1930.03680.149311.936380.073726.3859
212.8848-0.943-0.42321.6384-0.07721.14980.01590.08250.2831-0.0373-0.0258-0.03430.05960.07210.00250.12350.0081-0.03270.11010.01590.13119.772688.156216.3884
225.06140.39542.90266.65443.7836.3627-0.06650.5555-1.0809-0.4128-0.06870.05491.2156-0.11510.16750.4331-0.03340.02210.1944-0.06530.32349.48371.926311.2702
231.2162-0.1567-0.05531.28140.12551.03470.09560.2510.4964-0.2171-0.2149-0.13650.04980.0263-0.06430.12650.0582-0.00080.14980.12310.217319.946691.30796.5408
241.256-0.62980.37240.80990.22180.8047-0.0640.03540.0571-0.2598-0.1416-0.3807-0.12680.1254-0.00390.21970.06510.03690.06140.22970.510312.2735108.91446.5488
255.3990.2390.20651.83430.71531.7042-0.0425-0.3272-0.16140.12210.04320.0790.3039-0.01620.08930.17780.0125-0.03920.13480.01510.109837.564775.497466.3151
266.7310.2989-4.21810.750.47614.6174-0.1366-0.0329-0.45130.1920.0701-0.13120.40520.01890.06520.2273-0.004-0.06340.1261-0.00890.183841.086967.063562.1277
272.496-2.32680.34844.76770.46011.24590.023-0.0448-0.0270.09910.095-0.2642-0.02950.1412-0.15140.0888-0.0162-0.03230.1218-0.00160.087142.684382.375866.3875
283.6014.3316-0.67945.3558-0.17512.98770.1499-0.09040.94090.00190.1071-0.591-0.44310.2573-0.06510.18-0.00060.06160.1068-0.06230.570840.1188107.149567.8741
294.831-1.4551-1.34836.04154.33817.1476-0.0478-0.39290.44620.2551-0.035-0.217-0.21730.1542-0.03850.1348-0.0078-0.04250.127-0.0060.127944.374795.097168.6804
301.6395-0.1140.38061.08210.20630.39250.01960.0639-0.057-0.0306-0.0093-0.02130.0044-0.0397-0.00850.14070.0024-0.02440.1452-0.00680.115234.06383.910460.3953
314.0873-1.3455-0.22154.8998-4.17844.0746-0.01090.34670.633-0.4831-0.2109-0.0523-0.56270.07610.32640.3139-0.0061-0.07060.18920.06810.214242.177498.657150.2163
322.87742.677-0.2965.8252-0.54810.973-0.00380.1659-0.0907-0.40810.01-0.1593-0.00870.25260.01080.17810.0205-0.01780.2102-0.01380.087741.937580.652752.4827
332.15330.18771.76852.2989-0.2491.52410.12010.2967-0.4406-0.593-0.02340.43890.2611-0.2176-0.01720.2299-0.0063-0.11010.1832-0.09720.223420.454875.255449.8618
341.55530.29970.39984.0048-0.05950.65960.09940.1117-0.1151-0.242-0.11510.1411-0.005-0.00380.00590.16820.0217-0.04750.1525-0.02820.10332.007378.877151.8121
353.1118-2.0967-1.77941.451.15691.53-0.17990.0693-0.0879-0.18080.04710.25240.2873-0.10560.1470.27650.0056-0.08160.1444-0.0390.232539.972461.772453.4125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:18)
2X-RAY DIFFRACTION2chain 'A' and (resseq 19:34)
3X-RAY DIFFRACTION3chain 'A' and (resseq 35:55)
4X-RAY DIFFRACTION4chain 'A' and (resseq 56:72)
5X-RAY DIFFRACTION5chain 'A' and (resseq 73:91)
6X-RAY DIFFRACTION6chain 'A' and (resseq 92:117)
7X-RAY DIFFRACTION7chain 'A' and (resseq 118:130)
8X-RAY DIFFRACTION8chain 'A' and (resseq 131:174)
9X-RAY DIFFRACTION9chain 'A' and (resseq 175:191)
10X-RAY DIFFRACTION10chain 'A' and (resseq 192:217)
11X-RAY DIFFRACTION11chain 'B' and (resseq -2:18)
12X-RAY DIFFRACTION12chain 'B' and (resseq 19:34)
13X-RAY DIFFRACTION13chain 'B' and (resseq 35:55)
14X-RAY DIFFRACTION14chain 'B' and (resseq 56:72)
15X-RAY DIFFRACTION15chain 'B' and (resseq 73:117)
16X-RAY DIFFRACTION16chain 'B' and (resseq 118:130)
17X-RAY DIFFRACTION17chain 'B' and (resseq 131:191)
18X-RAY DIFFRACTION18chain 'B' and (resseq 192:217)
19X-RAY DIFFRACTION19chain 'C' and (resseq 0:34)
20X-RAY DIFFRACTION20chain 'C' and (resseq 35:91)
21X-RAY DIFFRACTION21chain 'C' and (resseq 92:117)
22X-RAY DIFFRACTION22chain 'C' and (resseq 118:130)
23X-RAY DIFFRACTION23chain 'C' and (resseq 131:191)
24X-RAY DIFFRACTION24chain 'C' and (resseq 192:219)
25X-RAY DIFFRACTION25chain 'D' and (resseq 2:18)
26X-RAY DIFFRACTION26chain 'D' and (resseq 19:34)
27X-RAY DIFFRACTION27chain 'D' and (resseq 35:55)
28X-RAY DIFFRACTION28chain 'D' and (resseq 56:72)
29X-RAY DIFFRACTION29chain 'D' and (resseq 73:90)
30X-RAY DIFFRACTION30chain 'D' and (resseq 91:117)
31X-RAY DIFFRACTION31chain 'D' and (resseq 118:133)
32X-RAY DIFFRACTION32chain 'D' and (resseq 134:146)
33X-RAY DIFFRACTION33chain 'D' and (resseq 147:161)
34X-RAY DIFFRACTION34chain 'D' and (resseq 162:191)
35X-RAY DIFFRACTION35chain 'D' and (resseq 192:219)

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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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