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- PDB-7r2o: Crystal structure of a flavodiiron protein S262Y mutant in the ox... -

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Basic information

Entry
Database: PDB / ID: 7r2o
TitleCrystal structure of a flavodiiron protein S262Y mutant in the oxidized state from Escherichia coli
ComponentsAnaerobic nitric oxide reductase flavorubredoxin
KeywordsOXIDOREDUCTASE / flavodiiron / nitrosative stress / ROS / FMN / iron
Function / homology
Function and homology information


nitric oxide reductase activity / nitric oxide catabolic process / oxidoreductase activity, acting on other nitrogenous compounds as donors / response to nitric oxide / FMN binding / electron transfer activity / iron ion binding / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Anaerobic nitric oxide reductase flavorubredoxin / Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase ...Anaerobic nitric oxide reductase flavorubredoxin / Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily
Similarity search - Domain/homology
MU-OXO-DIIRON / FLAVIN MONONUCLEOTIDE / Anaerobic nitric oxide reductase flavorubredoxin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBorges, P.T. / Teixeira, M. / Romao, C.V. / Frazao, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of a flavodiiron protein S262Y mutant in the oxidized state from Escherichia coli
Authors: Borges, P.T. / Teixeira, M. / Romao, C.V. / Frazao, C.
History
DepositionFeb 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anaerobic nitric oxide reductase flavorubredoxin
B: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9987
Polymers108,7382
Non-polymers1,2605
Water10,305572
1
A: Anaerobic nitric oxide reductase flavorubredoxin
B: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin
B: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,99714
Polymers217,4764
Non-polymers2,52010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-45 kcal/mol
Surface area29950 Å2
3
A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0908
Polymers108,7382
Non-polymers1,3526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7100 Å2
ΔGint-69 kcal/mol
Surface area28130 Å2
MethodPISA
4
B: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules

B: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9066
Polymers108,7382
Non-polymers1,1684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6560 Å2
ΔGint-67 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.968, 64.019, 88.882
Angle α, β, γ (deg.)90.000, 120.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21A-853-

HOH

31A-871-

HOH

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Components

#1: Protein Anaerobic nitric oxide reductase flavorubredoxin / FlRd / FlavoRb


Mass: 54369.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46877
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate pH 5.6, 20-23% w/v PEG 4000 and 23-25% v/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.85→58.67 Å / Num. obs: 70227 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.992 / Net I/σ(I): 5.68
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 70227 / CC1/2: 0.385

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FlRd

Resolution: 1.85→58.67 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.94 / Stereochemistry target values: LS_WUNIT_K1
Details: THE REFINEMENT CONVERGED TO R-WORK AND R-FREE OF 0.187 AND 0.221, RESPECTIVELY. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET.
RfactorNum. reflection% reflection
Rfree0.1837 70199 100 %
Rwork0.1837 70199 -
obs0.1837 70199 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.47 Å2 / Biso mean: 33.0748 Å2 / Biso min: 16.75 Å2
Refinement stepCycle: final / Resolution: 1.85→58.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6439 0 97 572 7108
Biso mean--39.91 39.21 -
Num. residues----800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.346222810.34622281456299
1.87-1.890.334123520.334123524704100
1.89-1.920.328322880.328322884576100
1.92-1.940.316923390.316923394678100
1.94-1.970.311323370.311323374674100
1.97-1.990.306123090.306123094618100
1.99-2.020.298223350.298223354670100
2.02-2.050.286723480.286723484696100
2.05-2.080.276923080.276923084616100
2.08-2.120.272323420.272323424684100
2.12-2.150.251123380.251123384676100
2.15-2.190.244423450.244423454690100
2.19-2.240.236123280.236123284656100
2.24-2.280.23323230.23323234646100
2.28-2.330.221123540.221123544708100
2.33-2.390.226523180.226523184636100
2.39-2.440.213223420.213223424684100
2.45-2.510.204723090.204723094618100
2.51-2.590.198423480.198423484696100
2.59-2.670.190223770.190223774754100
2.67-2.760.18723050.18723054610100
2.76-2.870.176423640.176423644728100
2.87-3.010.171923320.171923324664100
3.01-3.160.158823360.15882336467299
3.16-3.360.151823640.151823644728100
3.36-3.620.1323320.1323324664100
3.62-3.990.122323640.122323644728100
3.99-4.560.113723820.113723824764100
4.56-5.750.136923650.13692365473099
5.75-58.670.17824340.1782434486899
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)
12.8940.3936-2.3251.42590.54233.7436-0.26950.2004-0.4490.08330.1960.04050.5223-0.31930.19530.2554-0.0109-0.00640.2643-0.01680.27465.0444-14.62314.7862
21.6493-1.4499-0.45882.13870.79961.964-0.1367-0.1803-0.13890.3797-0.08040.0426-0.0253-0.05020.19360.3174-0.04110.02240.2384-0.01980.294-12.1728-9.381828.4651
31.49710.0081-0.03911.16740.13861.3849-0.09850.1472-0.02360.02730.0429-0.02880.0619-0.0260.06590.2084-0.00120.00840.19380.01840.19948.9489-8.71718.6633
48.1923-0.7684-0.26564.6672-0.72912.6782-0.1252-0.7265-0.86830.27730.17690.13730.4288-0.0008-0.05660.3450.004-0.00650.2510.05640.35328.9388-15.589827.8388
50.9213-0.38140.09482.0383-0.11661.4249-0.0727-0.09240.01050.21740.121-0.2420.14520.068-0.06020.227-0.0015-0.02370.22670.01040.211611.3803-3.0426.3185
61.38680.2304-0.07050.86230.17221.5893-0.0522-0.17710.16330.0692-0.0002-0.0027-0.18040.230.04230.2076-0.0094-0.01550.2266-0.01240.227911.90864.676528.1629
73.6224-1.9047-1.26463.89381.90755.18450.21670.54530.2176-0.52810.0795-0.9459-0.36810.1099-0.18950.2556-0.01960.04080.30520.00570.352716.5508-2.16828.7297
81.1825-0.0808-0.28510.6070.09221.1834-0.0562-0.0331-0.1321-0.0297-0.02960.04660.1026-0.09730.09680.2094-0.0116-0.00410.21950.00150.1929-3.2528-3.892915.1617
91.68820.3994-0.88151.09310.01530.8452-0.0430.1290.14460.086-0.0260.0601-0.0478-0.10310.04010.21240.0018-0.02290.26050.02080.2214-7.68336.798714.3681
101.08550.3175-0.0510.71480.03590.8380.04090.125-0.0747-0.01350.02630.14520.19750.02850.00980.233-0.01410.00060.2187-0.02380.2018-3.9026-5.55138.8272
116.0869-1.826-1.26922.0142-0.01520.65630.18010.6957-0.06010.0016-0.1712-0.1033-0.0129-0.10490.05380.247-0.01830.00670.26180.01110.1876-16.67235.729711.14
123.145-0.366-0.74841.0926-0.35511.6215-0.13180.3545-0.2563-0.08090.02410.10180.128-0.18720.09040.2275-0.0440.00980.2424-0.04240.2433-34.88211.043925.0772
131.45870.0620.82210.437-0.17611.559-0.033-0.0125-0.03070.0463-0.01590.0037-0.0361-0.06770.02330.205-0.0043-0.01450.19030.01070.1892-28.13986.573731.1104
144.3706-0.70920.01541.44930.29033.75090.16830.27590.3265-0.11230.0419-0.1566-0.07980.1579-0.07370.2577-0.02840.00330.22710.030.2708-22.114311.948723.4292
152.56410.7035-1.27291.1451-0.99221.97550.22190.04380.28240.2359-0.08310.1576-0.4655-0.0475-0.07920.2481-0.01170.01330.24550.00540.2828-37.454412.392737.566
164.33460.4829-0.5582.35740.80232.12680.1132-0.08230.5047-0.0590.0105-0.0486-0.1366-0.2002-0.02630.2784-0.0072-0.01040.1780.03250.3013-28.916616.649427.6884
172.02830.1083-0.80031.0706-1.19993.2582-0.01270.69210.1783-0.04210.03560.1923-0.1533-0.6398-0.04270.25810.0206-0.01920.40710.03140.2758-44.07459.496623.1329
182.7004-0.05441.77991.5011-0.45593.5644-0.17410.46850.5826-0.03340.15950.1793-0.44990.31020.03990.2862-0.0562-0.03960.3290.06890.3165-50.0027-9.233314.5475
191.446-1.06180.41262.3869-0.3881.7379-0.0378-0.08880.21810.4128-0.2192-0.06840.05550.02550.29090.3372-0.0487-0.04460.25080.02120.3365-32.7997-14.280328.3782
201.4148-0.2768-0.02941.1019-0.0951.898-0.07930.16020.1057-0.0850.06920.0658-0.1349-0.02090.0150.2499-0.0252-0.06070.25660.01340.2854-53.9057-15.051518.5018
212.5309-0.3447-0.67932.71470.48781.2257-0.0064-0.09250.35660.05470.0980.0279-0.30150.0659-0.12270.2614-0.0008-0.00970.2263-0.01940.3028-54.2978-13.297925.8574
220.9933-0.057-0.18671.1609-0.33831.79640.0363-0.14410.03150.10030.06470.0627-0.1889-0.1301-0.09350.2096-0.019-0.00420.2353-0.02450.2336-57.1342-23.990929.6297
234.366-2.1857-0.92044.94971.49451.70110.00590.5817-0.3923-0.1955-0.30580.85840.2154-0.41350.09970.2622-0.0663-0.00020.4193-0.09090.3378-58.7151-30.751613.0818
240.9635-0.1356-0.33251.47790.00220.9145-0.0230.3024-0.0178-0.1342-0.04790.08890.0620.03290.03930.201-0.0262-0.03170.2636-0.02510.2154-50.9096-25.848213.9943
251.41860.19640.2861.728-0.23611.8208-0.07670.30210.3619-0.14920.0744-0.1013-0.18970.30890.0340.2348-0.0769-0.01470.33820.04970.2717-35.0765-13.149614.5667
261.59670.43020.64291.24290.13360.7702-0.03780.0012-0.152-0.1131-0.1082-0.06040.0385-0.15330.18920.2288-0.01850.0110.3035-0.07470.2667-36.4518-30.878215.0998
271.90880.1817-0.17460.6992-0.16511.29130.03410.35740.095-0.16350.0362-0.02380.15470.12350.02360.27-0.0254-0.02870.36460.02410.2358-42.2119-18.74747.9161
283.1455-0.62020.66180.9078-0.27640.4111-0.0390.4948-0.01460.01690.00840.23220.03010.240.01190.2596-0.0337-0.01420.392-0.02680.23-27.1499-28.461411.1006
292.32020.06641.13631.210.261.7045-0.12220.17830.1434-0.0120.0438-0.0618-0.12510.25720.09560.1987-0.031-0.00920.23410.03130.2306-9.7255-24.477325.9065
301.7440.1586-0.7850.4636-0.05511.3517-0.130.114-0.12690.05620.06360.00090.00440.04930.02270.2184-0.0141-0.0010.1965-0.00560.2396-18.1919-30.549430.7203
313.216-0.57942.52581.15170.4583.1110.2010.004-0.39020.04620.00170.12590.1761-0.0144-0.31530.1982-0.040.03060.1983-0.00470.2853-13.255-35.82929.0802
322.17390.70591.49081.6525-0.69322.50170.1139-0.0478-0.2875-0.1375-0.0019-0.20370.250.0028-0.05510.2404-0.01080.020.1714-0.02110.3023-16.1785-39.531131.1451
331.51090.07640.72840.72070.85322.18730.02280.0914-0.07830.0748-0.01720.00250.03460.4542-0.01650.23620.00060.00040.25380.01210.28750.2511-32.724931.6731
341.1381-0.47580.81221.70340.65834.63010.12820.9202-0.1061-0.0417-0.1418-0.29420.43020.7605-0.04780.28010.00980.04650.4724-0.04740.3406-3.2809-34.536516.7694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:15)A2 - 15
2X-RAY DIFFRACTION2(chain A and resid 16:33)A16 - 33
3X-RAY DIFFRACTION3(chain A and resid 34:52)A34 - 52
4X-RAY DIFFRACTION4(chain A and resid 53:69)A53 - 69
5X-RAY DIFFRACTION5(chain A and resid 70:106)A70 - 106
6X-RAY DIFFRACTION6(chain A and resid 107:129)A107 - 129
7X-RAY DIFFRACTION7(chain A and resid 130:138)A130 - 138
8X-RAY DIFFRACTION8(chain A and resid 139:190)A139 - 190
9X-RAY DIFFRACTION9(chain A and resid 191:218)A191 - 218
10X-RAY DIFFRACTION10(chain A and resid 219:239)A219 - 239
11X-RAY DIFFRACTION11(chain A and resid 240:251)A240 - 251
12X-RAY DIFFRACTION12(chain A and resid 252:298)A252 - 298
13X-RAY DIFFRACTION13(chain A and resid 299:328)A299 - 328
14X-RAY DIFFRACTION14(chain A and resid 329:341)A329 - 341
15X-RAY DIFFRACTION15(chain A and resid 342:356)A342 - 356
16X-RAY DIFFRACTION16(chain A and resid 357:370)A357 - 370
17X-RAY DIFFRACTION17(chain A and resid 371:402)A371 - 402
18X-RAY DIFFRACTION18(chain B and resid 2:15)B2 - 15
19X-RAY DIFFRACTION19(chain B and resid 16:33)B16 - 33
20X-RAY DIFFRACTION20(chain B and resid 34:52)B34 - 52
21X-RAY DIFFRACTION21(chain B and resid 53:83)B53 - 83
22X-RAY DIFFRACTION22(chain B and resid 84:124)B84 - 124
23X-RAY DIFFRACTION23(chain B and resid 125:131)B125 - 131
24X-RAY DIFFRACTION24(chain B and resid 132:164)B132 - 164
25X-RAY DIFFRACTION25(chain B and resid 165:191)B165 - 191
26X-RAY DIFFRACTION26(chain B and resid 192:216)B192 - 216
27X-RAY DIFFRACTION27(chain B and resid 217:237)B217 - 237
28X-RAY DIFFRACTION28(chain B and resid 238:253)B238 - 253
29X-RAY DIFFRACTION29(chain B and resid 254:298)B254 - 298
30X-RAY DIFFRACTION30(chain B and resid 299:333)B299 - 333
31X-RAY DIFFRACTION31(chain B and resid 334:350)B334 - 350
32X-RAY DIFFRACTION32(chain B and resid 351:366)B351 - 366
33X-RAY DIFFRACTION33(chain B and resid 367:382)B367 - 382
34X-RAY DIFFRACTION34(chain B and resid 383:402)B383 - 402

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  • 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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