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- PDB-7r2r: Crystal structure of a flavodiiron protein D52K/S262Y mutant in t... -

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Basic information

Entry
Database: PDB / ID: 7r2r
TitleCrystal structure of a flavodiiron protein D52K/S262Y mutant in the reduced 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
: / FLAVIN MONONUCLEOTIDE / OXYGEN ATOM / OXYGEN MOLECULE / Anaerobic nitric oxide reductase flavorubredoxin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.198 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/S262Y mutant in the reduced 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 ...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)109,99812
Polymers108,7662
Non-polymers1,23210
Water6,449358
1
A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,99812
Polymers108,7662
Non-polymers1,23210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7180 Å2
ΔGint-79 kcal/mol
Surface area29000 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)109,99812
Polymers108,7662
Non-polymers1,23210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7160 Å2
ΔGint-79 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.955, 64.240, 146.850
Angle α, β, γ (deg.)90.000, 91.380, 90.000
Int Tables number5
Space group name H-MI121
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 - 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: 54383.191 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 , 5 types, 368 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.: 358 / 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 PEG4000 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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.198→77.44 Å / Num. obs: 42882 / % possible obs: 98.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 24.42 Å2 / CC1/2: 0.984 / Net I/σ(I): 6.3
Reflection shellResolution: 2.2→2.29 Å / Num. unique obs: 6547 / CC1/2: 0.585

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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: 2.198→44.781 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 16.74 / Phase error: 17.67 / Stereochemistry target values: ML
Details: THE REFINEMENT CONVERGED TO R-WORK AND R-FREE OF 0.209 AND 0.262, RESPECTIVELY. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET.
RfactorNum. reflection% reflection
Rfree0.262 42882 100 %
Rwork0.209 42882 -
obs-42882 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.68 Å2 / Biso mean: 28.22 Å2 / Biso min: 5.14 Å2
Refinement stepCycle: final / Resolution: 2.198→44.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 72 358 6872
Biso mean--23.33 31.86 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086700
X-RAY DIFFRACTIONf_angle_d0.5619082
X-RAY DIFFRACTIONf_chiral_restr0.022986
X-RAY DIFFRACTIONf_plane_restr0.0021174
X-RAY DIFFRACTIONf_dihedral_angle_d10.8192428
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3880X-RAY DIFFRACTION3.793TORSIONAL
12B3880X-RAY DIFFRACTION3.793TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1984-2.22340.302910660.3029106673
2.2234-2.24960.265814390.26581439100
2.2496-2.2770.258914280.25891428100
2.277-2.30580.254714300.25471430100
2.3058-2.33620.263314120.26331412100
2.3362-2.36820.247414260.24741426100
2.3682-2.4020.24914580.2491458100
2.402-2.43790.237814130.23781413100
2.4379-2.4760.229514280.22951428100
2.476-2.51650.222314470.22231447100
2.5165-2.55990.215114300.21511430100
2.5599-2.60650.229614280.22961428100
2.6065-2.65660.22414200.2241420100
2.6566-2.71080.225514390.22551439100
2.7108-2.76980.221814600.22181460100
2.7698-2.83420.212814220.21281422100
2.8342-2.9050.213414500.21341450100
2.905-2.98360.215314360.21531436100
2.9836-3.07140.229414270.22941427100
3.0714-3.17050.202914430.20291443100
3.1705-3.28370.205814220.20581422100
3.2837-3.41520.1814400.181440100
3.4152-3.57050.171714730.17171473100
3.5705-3.75870.156414310.15641431100
3.7587-3.99410.143914430.14391443100
3.9941-4.30220.138814530.13881453100
4.3022-4.73470.137914560.13791456100
4.7347-5.41890.153314780.15331478100
5.4189-6.82330.184114620.18411462100
6.8233-44.7810.165915220.16591522100
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)
10.0113-0.0065-0.05260.0276-0.03470.21820.2-0.0411-0.09540.2145-0.032-0.19780.2592-0.1249-0.00660.19210.0301-0.03620.1752-0.00110.1995-28.8554-36.5695-10.0169
20.00730.0025-0.0099-0.0010.0020.00960.20870.05250.0828-0.0724-0.2754-0.0183-0.0055-0.058900.3369-0.0539-0.06450.4670.08840.5408-11.0285-25.7017-4.6965
30.07220.0452-0.1750.1790.01710.4827-0.14550.1054-0.16920.1620.0741-0.1404-0.0741-0.2667-0.12610.14230.033-0.07470.0110.05370.1444-30.0272-30.9688-14.157
40.12430.01870.11140.05070.01580.09030.03540.0814-0.3121-0.09270.1233-0.10410.22220.14720.02730.2340.03270.00870.1095-0.02860.194-25.3754-37.6542-22.1052
50.0669-0.037-0.08180.06470.02060.08780.0263-0.0694-0.1638-0.08290.0001-0.13330.17350.0991-0.0170.17540.01610.02920.1207-0.00770.2132-26.8318-26.3238-21.0435
60.10080.10620.01460.45950.21090.39330.01550.15060.1004-0.05620.0914-0.04010.0212-0.05810.09320.16820.0134-0.01820.15250.03890.1471-28.1359-18.9923-25.2171
70.23850.1577-0.11910.1770.13140.2093-0.0036-0.0262-0.13530.0266-0.00250.0003-0.037-0.0062-0.0230.0984-0.0118-0.00240.12820.03290.1543-32.3241-25.1649-7.2517
80.0083-0.0045-0.01030.0020.00560.00980.0517-0.0163-0.02020.1940.0414-0.07530.1440.1065-00.173-0.0103-0.04970.25070.03810.303-21.9886-26.45144.6251
90.09130.01150.02280.0095-0.0580.11270.0327-0.0772-0.1811-0.0031-0.0545-0.0758-0.1121-0.1005-0.03760.10580.045-0.01030.12280.01140.1123-32.3909-19.4896-1.2739
100.0073-0.0247-0.01430.160.1480.3119-0.008-0.1098-0.0035-0.0186-0.07870.0958-0.0626-0.1626-0.1333-0.24720.02930.33050.36090.025-0.0598-26.6473-15.86798.8775
110.11070.08660.06740.16520.19230.21870.0584-0.1979-0.1307-0.01870.1323-0.04960.2806-0.08420.10580.1237-0.0216-0.00310.17980.0350.129-4.6505-19.748619.5604
120.0142-0.012-0.04890.00910.04190.111-0.139-0.1058-0.1720.0170.1233-0.11470.0832-0.03750.04220.0977-0.01050.04820.14930.00510.1122-4.2403-17.38028.4738
130.19780.10430.08930.06130.04740.0416-0.089-0.02320.3259-0.06820.03030.12830.0424-0.1333-0.02080.13260.02930.01390.13020.03060.136-12.8867-9.76226.2418
140.03130.0210.00910.07250.02410.03850.09630.00690.1985-0.0666-0.071-0.091-0.00890.02260.0120.15040.0370.00350.1145-0.01360.14951.7237-7.814213.607
150.14120.0472-0.15630.7242-0.1260.226-0.0722-0.37950.19390.1396-0.2184-0.2146-0.243-0.2224-0.24880.14040.07260.03950.2174-0.10410.1123-2.8754-12.631527.111
160.04330.01610.01970.0595-0.01270.0083-0.08070.02360.2050.04860.1507-0.0216-0.1435-0.085100.230.04090.0280.18360.02230.1526-5.6594-30.755830.1671
170.010.0017-0.004-0.00220.00220.0019-0.2506-0.0474-0.1264-0.0674-0.2234-0.1024-0.0443-0.0415-0.00010.40390.0397-0.00590.32170.00860.405-1.4411-41.5311.9548
180.0505-0.06750.0010.05910.01770.00620.0033-0.03350.10010.00420.00420.18530.0623-0.102700.29690.006-0.00890.14520.00640.1679-2.6119-36.348633.192
190.1586-0.0554-0.16530.03240.06180.4087-0.0255-0.07220.2404-0.07960.1498-0.2756-0.25790.18350.01710.2934-0.0156-0.05270.15450.03140.27016.5893-29.679933.108
200.3043-0.01910.00550.0220.02710.0977-0.0280.19280.3119-0.1211-0.07530.1882-0.2529-0.0521-0.00140.24940.01470.03010.1226-0.01030.19134.9017-41.012533.7777
210.3594-0.3966-0.18951.08480.66430.5475-0.0722-0.10670.0322-0.02220.2289-0.24050.15860.09540.34130.1662-0.0278-0.04560.15470.04910.11477.9105-48.337936.9311
220.20670.0415-0.00710.046-0.04180.02620.0586-0.0628-0.05470.01790.02640.0389-0.1119-0.24610.05720.18150.0643-0.00070.16270.03460.1281-9.7876-42.123131.7853
230.46180.0669-0.15480.0099-0.02580.0536-0.09120.0156-0.0719-0.1273-0.1080.0804-0.18180.0674-0.05120.23430.0045-0.0730.22770.00460.1246-14.9961-40.731316.9334
240.1553-0.0046-0.11170.13190.12060.3270.0033-0.0893-0.1198-0.144-0.08260.1044-0.1172-0.2789-0.32250.0007-0.11820.11430.06870.2042-0.1107-15.0728-47.733728.9007
250.0098-0.0136-0.00620.00260.00610.0045-0.0195-0.16930.05550.01340.0377-0.16080.2093-0.3163-00.1396-0.00520.05190.32450.03730.2085-21.0465-51.301618.7947
260.1259-0.00270.06680.19340.22570.29140.04730.0201-0.0069-0.08950.13730.0813-0.2713-0.46260.28180.08470.0236-0.00630.18040.06820.0759-19.2261-47.4495-5.6649
270.1433-0.00320.0812-0.02570.06710.1045-0.08870.00580.11490.02320.0974-0.0650.0346-0.0741-0.00130.1201-0.0023-0.0160.13360.01370.1398-9.4752-49.8538-0.4751
280.141-0.1221-0.08620.23870.16810.13140.11950.03840.15020.10010.2225-0.17550.2636-0.19410.03310.1957-0.0135-0.04050.19250.07550.2645-11.896-57.46258.1962
290.0715-0.00240.04610.0209-0.05440.1677-0.0193-0.0251-0.0838-0.03350.0023-0.12180.1462-0.14710.00080.1658-0.003-0.00990.1040.00880.1701-10.9653-59.4439-8.1942
300.1146-0.1981-0.06480.47390.14130.06520.09570.0201-0.2303-0.1309-0.11910.01420.1182-0.44250.03370.1431-0.0774-0.03810.30720.01580.2247-24.9772-54.5401-10.921
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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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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