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- PDB-7r0f: Crystal structure of a flavodiiron protein D52K mutant in the oxi... -

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Basic information

Entry
Database: PDB / ID: 7r0f
TitleCrystal structure of a flavodiiron protein D52K 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 / oxidoreductase activity, acting on other nitrogenous compounds as donors / nitric oxide catabolic process / response to nitric oxide / FMN binding / oxidoreductase activity / 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
: / FLAVIN MONONUCLEOTIDE / OXYGEN ATOM / OXYGEN MOLECULE / Anaerobic nitric oxide reductase flavorubredoxin
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 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 D52K mutant in the oxidized state from Escherichia coli
Authors: Borges, P.T. / Teixeira, M. / Romao, C.V. / Frazao, C.
History
DepositionFeb 2, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)109,84612
Polymers108,6142
Non-polymers1,23210
Water9,242513
1
A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,84612
Polymers108,6142
Non-polymers1,23210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6900 Å2
ΔGint-80 kcal/mol
Surface area28920 Å2
MethodPISA
2
B: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules

B: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,84612
Polymers108,6142
Non-polymers1,23210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6890 Å2
ΔGint-79 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.958, 64.051, 146.480
Angle α, β, γ (deg.)90.000, 91.140, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-793-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HOH / End label comp-ID: HOH / Auth seq-ID: 1 - 603 / Label seq-ID: 1

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - M
2chain BBB - N

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 54307.098 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

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Non-polymers , 5 types, 523 molecules

#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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.93 Å3/Da / Density % sol: 36.21 %
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: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.978→76.81 Å / Num. obs: 56529 / % possible obs: 95.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.63 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.088 / Net I/σ(I): 5.8
Reflection shellResolution: 1.98→2.07 Å / Num. unique obs: 8571 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIXdev_1436refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FlRD

Resolution: 1.978→73.32 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 15.46 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 54918 100 %
Rwork0.2054 54918 -
obs0.2054 54918 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.87 Å2 / Biso mean: 28.61 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 1.978→73.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6446 0 72 513 7031
Biso mean--21.5 35.23 -
Num. residues----802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016702
X-RAY DIFFRACTIONf_angle_d0.589082
X-RAY DIFFRACTIONf_chiral_restr0.023988
X-RAY DIFFRACTIONf_plane_restr0.0021174
X-RAY DIFFRACTIONf_dihedral_angle_d11.2392432
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3909X-RAY DIFFRACTION3.83TORSIONAL
12B3909X-RAY DIFFRACTION3.83TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9781-2.00060.36353110.363531116
2.0006-2.02410.293118350.2931183596
2.0241-2.04880.270218730.2702187398
2.0488-2.07470.266518800.2665188098
2.0747-2.1020.270818580.2708185897
2.102-2.13080.252518700.2525187097
2.1308-2.16130.252818910.2528189197
2.1613-2.19350.236118640.2361186497
2.1935-2.22780.241718480.2417184897
2.2278-2.26430.238818730.2388187397
2.2643-2.30340.247118600.2471186097
2.3034-2.34530.231618710.2316187197
2.3453-2.39040.231118460.2311184696
2.3904-2.43920.213918780.2139187898
2.4392-2.49220.228919090.2289190998
2.4922-2.55020.221318520.2213185298
2.5502-2.6140.217318850.2173188598
2.614-2.68460.216718880.2167188898
2.6846-2.76360.20818920.208189298
2.7636-2.85290.209118660.2091186698
2.8529-2.95480.212219190.2122191999
2.9548-3.07310.210718870.2107188797
3.0731-3.2130.19218790.192187997
3.213-3.38240.184618910.1846189198
3.3824-3.59430.177219160.1772191699
3.5943-3.87180.17119090.171190998
3.8718-4.26140.165718950.1657189597
4.2614-4.87790.160118770.1601187796
4.8779-6.14520.184119470.1841194798
6.1452-73.320.212319480.2123194897
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)
10.01970.0554-0.05360.1887-0.03160.23030.1218-0.1057-0.234-0.10040.0558-0.05590.2708-0.07070.00270.17980.0262-0.01380.15420.00740.2365-28.6682-36.6644-9.9989
20.0223-0.0029-0.0317-0.0076-0.0010.03720.526-0.3492-0.1446-0.2498-0.0196-0.07480.1029-0.015900.2078-0.02370.02080.23530.03510.3115-11.125-25.763-4.7356
30.05490.083-0.08570.2781-0.01340.452-0.0391-0.2665-0.18680.02080.1907-0.0643-0.1651-0.35840.04670.11380.0352-0.01890.12350.01580.1739-29.8534-31.0993-14.1358
40.0752-0.05580.05410.1769-0.03890.11810.2723-0.0245-0.5624-0.25670.0275-0.12270.25350.25330.0030.27760.0155-0.02890.1887-0.02580.2499-25.2037-37.6643-21.9889
50.2408-0.1561-0.26680.19950.03630.31560.1145-0.0435-0.1824-0.09380.0077-0.02890.29110.19630.00020.19250.02060.02840.18360.01330.1969-26.6923-26.4152-20.9251
60.25850.1192-0.20080.1142-0.19750.5486-0.05140.18940.0901-0.05750.0045-0.050.006-0.0455-0.01240.12450.0217-0.00930.15360.00960.1058-28.0035-19.165-25.0493
70.33030.1037-0.22720.08410.09990.3674-0.0003-0.0485-0.09150.05180.01570.0103-0.0048-0.0181-00.1211-0.0054-0.00150.15510.03150.1409-32.1453-25.3206-7.2125
80.0094-0.0039-0.0070.10020.03660.03410.14320.0885-0.19630.3058-0.3432-0.1507-0.09870.00690.00040.1483-0.0074-0.04330.2366-0.00310.2214-21.7694-26.60614.5733
90.21650.06490.2548-0.01020.16720.1677-0.0216-0.0626-0.03470.0501-0.005-0.00280.0031-0.084400.10520.03240.01580.1605-0.00110.1591-32.1774-19.6811-1.2648
100.01790.07170.11570.90840.42211.05790.038-0.27570.2783-0.4349-0.1680.1992-0.1442-0.5302-0.1372-0.5260.18430.23770.37710.0010.1557-26.4695-16.11678.8139
110.38040.2440.45740.60830.15850.52670.2201-0.3268-0.37440.06390.0034-0.0750.1686-0.18070.09740.1424-0.0245-0.01720.18260.01870.1457-4.8178-19.858619.4859
120.24170.22020.0020.00950.14480.2838-0.253-0.102-0.0128-0.10190.1718-0.11240.0279-0.00970.02060.11910.04070.02810.138-0.0330.1592-4.1692-17.52298.4228
130.27720.0894-0.20660.0677-0.11210.1528-0.02640.28140.3898-0.02640.0359-0.14390.0736-0.02380.00670.16550.047-0.00730.12420.04280.1538-12.7491-9.96486.2299
140.1772-0.07130.21310.1707-0.02170.1611-0.0775-0.1460.4030.0126-0.0385-0.135-0.172-0.1466-0.0230.17660.03120.00750.098-0.00520.21641.7228-7.971813.5782
150.84710.9003-0.41831.1842-0.11790.68290.093-0.76660.19990.0698-0.1668-0.2622-0.0617-0.3168-0.33190.16620.06280.00490.3929-0.11020.1035-2.818-12.884226.9496
160.1593-0.20280.1470.2367-0.18320.09090.0409-0.02810.07690.0143-0.0108-0.1673-0.5787-0.00320.00130.2520.0184-0.00570.20930.01420.183-5.3412-30.701429.95
170.0406-0.00010.0197-0.00110.00520.0147-0.31810.2106-0.7968-0.036-0.21760.0180.0405-0.1754-0.00010.34830.08950.07250.27290.01360.2879-1.334-41.574511.9917
180.379-0.3597-0.06290.3920.04350.00740.1205-0.07890.0065-0.01610.0874-0.00090.007-0.151200.2223-0.01630.00130.14170.01540.1475-2.2916-36.275332.9526
190.1158-0.09940.04920.1102-0.04320.0643-0.08870.13090.0325-0.05970.014-0.264-0.6660.06310.00010.3348-0.0259-0.07070.1994-0.00740.23826.7865-29.700432.7021
200.25020.0717-0.1770.3097-0.12920.12020.08040.11050.3013-0.03560.0168-0.0804-0.0989-0.031-00.2024-0.00810.03140.18310.03010.20165.1756-40.96533.4875
210.5388-0.40950.17030.35720.04640.3667-0.0636-0.14030.0322-0.04610.0951-0.05850.12540.07690.01710.1913-0.0232-0.04330.17180.04560.16438.1509-48.211636.6384
220.53790.06280.2370.07630.25520.47010.0577-0.001-0.0473-0.02870.03480.1366-0.0272-0.21630.0010.19830.04110.00530.22750.0310.1794-9.4642-42.001731.5646
230.0452-0.0182-0.02010.02770.02620.04060.19010.0957-0.1884-0.2102-0.1523-0.0657-0.4912-0.09740.00010.2237-0.0147-0.0270.26870.01930.1714-14.6655-40.614716.7565
240.08530.13250.14130.2093-0.14840.3530.0766-0.1314-0.05450.0324-0.00930.00250.0839-0.15990.0080.1416-0.04840.00450.18160.04560.1212-14.7636-47.562428.7123
251.2364-1.35250.30172.9759-0.25250.1006-0.3946-0.4671-0.06980.67210.0432-0.39420.3482-0.479-0.02050.1533-0.02330.06930.29830.06580.1752-20.7952-51.035418.7391
260.262-0.39460.13820.57340.1930.91080.00620.0590.0944-0.09220.05860.0362-0.2718-0.26510.08380.15590.0077-0.01960.14890.0360.1209-19.383-47.4134-5.36
270.1355-0.0956-0.0733-0.00940.07390.17830.00790.03220.00260.01110.0903-0.02860.0348-0.147500.1769-0.0337-0.01230.15380.01460.1719-9.4045-49.7717-0.4875
280.22230.0195-0.17490.57180.33950.38280.0589-0.2566-0.3319-0.01120.0132-0.33430.51720.03210.12850.2741-0.0658-0.07650.22260.10960.2121-11.7457-57.31238.0949
290.3246-0.0640.46420.0172-0.03031.028-0.0947-0.219-0.1405-0.2048-0.0259-0.02550.3189-0.3549-0.13940.2605-0.0241-0.0337-0.0280.0150.179-11.0343-59.338-8.0991
300.1971-0.0948-0.12750.47210.08470.25640.0940.1288-0.2669-0.2787-0.1295-0.02130.3061-0.65710.00750.1977-0.1011-0.01870.30450.05790.2074-24.9963-54.3409-10.7317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:20)A2 - 20
2X-RAY DIFFRACTION2(chain A and resid 21:28)A21 - 28
3X-RAY DIFFRACTION3(chain A and resid 29:52)A29 - 52
4X-RAY DIFFRACTION4(chain A and resid 53:69)A53 - 69
5X-RAY DIFFRACTION5(chain A and resid 70:91)A70 - 91
6X-RAY DIFFRACTION6(chain A and resid 92:131)A92 - 131
7X-RAY DIFFRACTION7(chain A and resid 132:186)A132 - 186
8X-RAY DIFFRACTION8(chain A and resid 187:194)A187 - 194
9X-RAY DIFFRACTION9(chain A and resid 195:239)A195 - 239
10X-RAY DIFFRACTION10(chain A and resid 240:251)A240 - 251
11X-RAY DIFFRACTION11(chain A and resid 252:291)A252 - 291
12X-RAY DIFFRACTION12(chain A and resid 292:327)A292 - 327
13X-RAY DIFFRACTION13(chain A and resid 328:340)A328 - 340
14X-RAY DIFFRACTION14(chain A and resid 341:375)A341 - 375
15X-RAY DIFFRACTION15(chain A and resid 376:400)A376 - 400
16X-RAY DIFFRACTION16(chain B and resid 2:20)B2 - 20
17X-RAY DIFFRACTION17(chain B and resid 21:28)B21 - 28
18X-RAY DIFFRACTION18(chain B and resid 29:52)B29 - 52
19X-RAY DIFFRACTION19(chain B and resid 53:69)B53 - 69
20X-RAY DIFFRACTION20(chain B and resid 70:91)B70 - 91
21X-RAY DIFFRACTION21(chain B and resid 92:131)B92 - 131
22X-RAY DIFFRACTION22(chain B and resid 132:186)B132 - 186
23X-RAY DIFFRACTION23(chain B and resid 187:194)B187 - 194
24X-RAY DIFFRACTION24(chain B and resid 195:239)B195 - 239
25X-RAY DIFFRACTION25(chain B and resid 240:251)B240 - 251
26X-RAY DIFFRACTION26(chain B and resid 252:291)B252 - 291
27X-RAY DIFFRACTION27(chain B and resid 292:327)B292 - 327
28X-RAY DIFFRACTION28(chain B and resid 328:340)B328 - 340
29X-RAY DIFFRACTION29(chain B and resid 341:375)B341 - 375
30X-RAY DIFFRACTION30(chain B and resid 376:400)B376 - 400

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