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- PDB-7r2s: Crystal structure of a flavodiiron protein D52K mutant from Esche... -

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Basic information

Entry
Database: PDB / ID: 7r2s
TitleCrystal structure of a flavodiiron protein D52K mutant from Escherichia coli pressurized with krypton gas
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 / oxidoreductase 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 / KRYPTON / OXYGEN ATOM / OXYGEN MOLECULE / Anaerobic nitric oxide reductase flavorubredoxin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 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 from Escherichia coli pressurized with krypton gas
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 ...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

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)110,31717
Polymers108,6142
Non-polymers1,70315
Water6,864381
1
A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,34918
Polymers108,6142
Non-polymers1,73516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8130 Å2
ΔGint-90 kcal/mol
Surface area28700 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)110,28516
Polymers108,6142
Non-polymers1,67114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7900 Å2
ΔGint-91 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.952, 64.425, 147.080
Angle α, β, γ (deg.)90.000, 91.460, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

21A-746-

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: SER / Beg label comp-ID: SER / End auth comp-ID: HOH / End label comp-ID: HOH / Auth seq-ID: 2 - 603 / Label seq-ID: 2

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - R
2chain BBB - S

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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 (strain K12) (bacteria)
Strain: K12 / Gene: norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q46877

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Non-polymers , 6 types, 396 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-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Kr
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 1.94 Å3/Da / Density % sol: 36.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
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: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.194→52.34 Å / Num. obs: 41634 / % possible obs: 96.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 21.67 Å2 / CC1/2: 0.987 / Net I/σ(I): 5.7
Reflection shellResolution: 2.2→2.3 Å / Num. unique obs: 6564 / CC1/2: 0.645

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Processing

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

Resolution: 2.194→52.34 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 16.84 / Phase error: 22.51 / Stereochemistry target values: ML
Details: THE REFINEMENT CONVERGED TO R-WORK AND R-FREE OF 0.254 AND 0.295, RESPECTIVELY. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET.
RfactorNum. reflection% reflection
Rfree0.295 41634 100 %
Rwork0.254 41634 -
obs-41634 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.82 Å2 / Biso mean: 27.2 Å2 / Biso min: 4.69 Å2
Refinement stepCycle: final / Resolution: 2.194→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6430 0 76 381 6887
Biso mean--21 28.38 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136661
X-RAY DIFFRACTIONf_angle_d0.5729026
X-RAY DIFFRACTIONf_chiral_restr0.022984
X-RAY DIFFRACTIONf_plane_restr0.0031164
X-RAY DIFFRACTIONf_dihedral_angle_d11.0152410
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3902X-RAY DIFFRACTION2.337TORSIONAL
12B3902X-RAY DIFFRACTION2.337TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.194-2.21870.310811830.3108118381
2.2187-2.24480.272513840.2725138497
2.2448-2.27220.270613970.2706139797
2.2722-2.30090.247713860.2477138698
2.3009-2.33120.275113850.2751138597
2.3312-2.36310.238313890.2383138997
2.3631-2.39690.236814020.2368140296
2.3969-2.43270.24713530.247135396
2.4327-2.47070.253113780.2531137897
2.4707-2.51120.260414090.2604140997
2.5112-2.55450.260813660.2608136696
2.5545-2.60090.250113950.2501139596
2.6009-2.6510.267913630.2679136397
2.651-2.70510.250114090.2501140998
2.7051-2.76390.239813980.2398139897
2.7639-2.82820.253813910.2538139197
2.8282-2.89890.269614060.2696140697
2.8989-2.97730.257214010.2572140197
2.9773-3.06490.247113940.2471139498
3.0649-3.16380.231313940.2313139497
3.1638-3.27680.244613930.2446139397
3.2768-3.4080.221114000.2211140096
3.408-3.56310.232514080.2325140897
3.5631-3.75090.230913920.2309139298
3.7509-3.98580.206514040.2065140497
3.9858-4.29340.197214060.1972140697
4.2934-4.72520.193713880.1937138895
4.7252-5.40840.217814030.2178140395
5.4084-6.81160.246814230.2468142397
6.8116-52.340.232714340.2327143494
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)
10.00670.0053-0.01870.019-0.01530.0441-0.0688-0.0448-0.0656-0.02570.0818-0.15110.1171-0.0736-0.00050.1365-0.00190.01780.1526-0.00120.2471-28.5644-36.5638-10.1137
20.0022-0.0013-0.0007-0.00020.00140.00440.11990.00530.03220.03890.0326-0.051-0.0108-0.022800.2335-0.0442-0.00480.21380.0410.3032-11.0548-25.5993-4.7151
30.042-0.0101-0.03420.01160.01450.03320.02550.084-0.08870.1321-0.01830.0464-0.0858-0.1787-0.00180.14920.0069-0.01710.1382-0.00750.1937-29.7748-30.9862-14.2481
40.0540.01010.06240.14780.16220.41550.08240.0337-0.0455-0.14730.0898-0.1220.00410.02960.03150.4012-0.0015-0.07740.1204-0.02310.1888-25.1754-37.4449-22.3551
50.05320.0104-0.08070.006-0.01940.113-0.1651-0.0264-0.0824-0.0750.04590.03280.17970.1353-0.0190.15770.03490.02360.0957-0.01330.1967-26.6262-26.224-21.0444
60.01850.0011-0.01850.0373-0.02360.0434-0.11140.08130.0377-0.10960.16310.12380.0965-0.01590.00060.20240.0213-0.03520.1640.02190.1941-27.9311-18.9601-25.1973
70.01010.01980.00710.09410.1190.15310.013-0.122-0.11380.0141-0.01460.0707-0.035-0.0783-0.01920.1097-0.0212-0.00610.19740.06610.173-32.1149-25.2292-7.327
80.0072-0.0053-0.00320.00340.00050.0012-0.00320.0398-0.00910.0608-0.0448-0.0371-0.0249-0.0236-00.136-0.0218-0.06430.15790.05160.2938-21.6865-26.50984.4961
90.0277-0.0120.03780.0304-0.02070.03650.0061-0.1206-0.01290.092-0.00010.03460.0422-0.171-00.13940.0072-0.04660.2175-0.01430.201-32.1833-19.5985-1.3036
100.0056-0.0104-0.03050.01470.05250.1558-0.05370.0502-0.0424-0.0421-0.01970.01110.0342-0.1023-0.1066-0.11760.11030.19620.33150.06480.0698-26.4661-16.05528.8549
110.16320.1-0.0030.33070.08550.03350.0565-0.2659-0.07080.02610.1207-0.08340.1451-0.15240.09430.1138-0.01740.00760.18790.02270.0919-4.7882-19.691819.4844
120.0063-0.00320.02530.0194-0.04210.0994-0.1268-0.17060.0413-0.0090.187-0.05410.0645-0.04110.01110.11570.03580.02970.192-0.01120.1192-4.1759-17.30868.4168
130.04530.04660.03590.05780.0490.06780.00070.05710.0871-0.1258-0.0472-0.03820.03680.0735-0.06630.14250.05080.00370.08090.18520.1485-12.8942-9.76286.0396
140.0869-0.02340.08030.0166-0.01010.266-0.01180.01230.1241-0.0728-0.0585-0.113-0.1075-0.1671-0.08650.20770.037-0.0039-0.0402-0.02510.11771.6387-7.714913.5716
150.008-0.0049-0.01010.0795-0.01330.04850.0054-0.10740.0514-0.0418-0.0453-0.03210.0209-0.1764-0.02510.07350.02830.05020.2934-0.09930.1651-3.6574-12.334127.2183
160.0266-0.00120.01820.0045-0.00420.0102-0.10520.0137-0.0383-0.01250.1028-0.0485-0.1253-0.0416-00.25130.0005-0.02750.20420.04130.2139-5.4112-30.629329.8613
170.0043-0.00170.00160.00180.00050.00120.0007-0-0.08560.0261-0.02530.0504-0.02870.0083-00.53310.1161-0.04350.2864-0.05030.2954-1.3714-41.580611.9542
180.0225-0.01290.00120.02570.00240.0090.1307-0.08170.01510.0717-0.09940.0766-0.0729-0.11790.00060.2284-0.00920.00150.17510.00090.1676-2.4119-36.202932.9326
190.00860.01030.00640.02390.01420.0234-0.0682-0.0888-0.0709-0.06190.1422-0.1551-0.0596-0.010.00040.36420.0169-0.12270.1692-0.01290.24466.8698-29.752932.9646
200.021-0.0054-0.01010.0275-0.00580.00390.02330.17210.14850.05170.02560.0611-0.07720.0391-00.16480.00610.01370.16440.00930.13035.0261-40.979133.5567
210.0605-0.05060.01890.0412-0.03040.0288-0.0932-0.0731-0.04140.08260.0844-0.06180.1422-0.0021-0.00170.2006-0.0306-0.05480.15570.0410.17517.9656-48.242236.7603
220.10880.0050.04310.02080.02230.02330.1418-0.0079-0.04150.08280.0320.0333-0.0541-0.13760.0080.22980.0393-0.00190.21460.0370.1322-9.6228-41.91431.5367
230.00620.0033-0.00230.002-0.00330.00320.0111-0.026-0.0605-0.0442-0.11040.0104-0.02720.0621-00.2057-0.00820.02470.2965-0.03710.1859-14.7306-40.530316.6252
240.01590.01760.03020.01060.01980.02980.0615-0.15170.07620.03510.0189-0.03990.075-0.16560.00010.1917-0.0311-0.02460.23980.02740.166-14.9208-47.49328.6304
250.09880.05310.05470.090.01470.0309-0.0045-0.0475-0.00870.0425-0.0258-0.0160.0257-0.0566-0.0146-0.0246-0.06570.14420.34770.070.071-20.8863-50.992918.5929
260.0703-0.0404-0.04150.24960.11650.085-0.0277-0.01250.0101-0.09880.0936-0.0491-0.1054-0.27360.01270.15550.0159-0.02560.22520.02130.1769-19.2931-47.4568-5.5237
270.03260.00330.02440.00230.01870.0307-0.03910.07910.0883-0.06670.06110.09810.1373-0.103300.1485-0.0426-0.02270.15270.01420.1675-9.3895-49.851-0.5596
280.1870.0471-0.0360.0091-0.00510.0988-0.0283-0.019-0.0069-0.0023-0.0414-0.06690.08490.0406-0.08580.3209-0.0621-0.10060.09410.16380.0149-11.6789-57.39338.229
290.0347-0.01230.03240.00380.0060.1115-0.0098-0.0738-0.0768-0.001-0.0205-0.11880.1112-0.0674-0.03630.2398-0.0771-0.0677-0.0630.01040.1475-10.9177-59.4622-8.1757
300.17640.1492-0.01630.28140.06240.0352-0.0499-0.0413-0.1798-0.08750.03180.02060.0621-0.20260.01410.1199-0.1221-0.02980.24320.0320.1986-25.4408-54.8047-10.3443
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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  • 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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