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- PDB-7r1j: Crystal structure of a flavodiiron protein S262Y mutant in the re... -

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Basic information

Entry
Database: PDB / ID: 7r1j
TitleCrystal structure of a flavodiiron protein 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: 1.901 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 reduced state from Escherichia coli
Authors: Borges, P.T. / Teixeira, M. / Romao, C.V. / Frazao, C.
History
DepositionFeb 3, 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)109,97012
Polymers108,7382
Non-polymers1,23210
Water13,890771
1
A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules

A: Anaerobic nitric oxide reductase flavorubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,97012
Polymers108,7382
Non-polymers1,23210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7300 Å2
ΔGint-87 kcal/mol
Surface area28740 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)109,97012
Polymers108,7382
Non-polymers1,23210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7210 Å2
ΔGint-86 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.972, 64.383, 146.820
Angle α, β, γ (deg.)90.000, 91.235, 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: 54369.098 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 , 5 types, 781 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.: 771 / 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: 36.37 %
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 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→76.8 Å / Num. obs: 65086 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.07 Å2 / CC1/2: 0.991 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 10367 / CC1/2: 0.638

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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: 1.901→75.567 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 17.81 / Phase error: 16.29 / Stereochemistry target values: ML
Details: THE REFINEMENT CONVERGED TO R-WORK AND R-FREE OF 0.196 AND 0.224, RESPECTIVELY. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET.
RfactorNum. reflection% reflection
Rfree0.224 64796 100 %
Rwork0.196 64796 -
obs-64796 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.6 Å2 / Biso mean: 23.04 Å2 / Biso min: 6.31 Å2
Refinement stepCycle: final / Resolution: 1.901→75.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 72 771 7283
Biso mean--19.85 32.22 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136722
X-RAY DIFFRACTIONf_angle_d0.6959118
X-RAY DIFFRACTIONf_chiral_restr0.027988
X-RAY DIFFRACTIONf_plane_restr0.0031182
X-RAY DIFFRACTIONf_dihedral_angle_d11.1742432
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3900X-RAY DIFFRACTION2.064TORSIONAL
12B3900X-RAY DIFFRACTION2.064TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.901-1.92220.271220420.2712204295
1.9222-1.94480.267221690.2672216999
1.9448-1.96860.252321300.2523213099
1.9686-1.99350.240621530.2406215399
1.9935-2.01970.225221550.2252215599
2.0197-2.04740.228821270.2288212799
2.0474-2.07660.224521740.2245217499
2.0766-2.10760.228221230.2282212399
2.1076-2.14060.21621240.216212498
2.1406-2.17570.211721310.2117213199
2.1757-2.21320.19821910.1982191100
2.2132-2.25340.18221310.182213199
2.2534-2.29680.191221800.19122180100
2.2968-2.34370.193421500.1934215099
2.3437-2.39460.199921470.1999214799
2.3946-2.45030.175421550.1754215599
2.4503-2.51160.177321230.1773212399
2.5116-2.57950.182221840.1822218499
2.5795-2.65540.186221360.1862213699
2.6554-2.74110.186121650.1861216599
2.7411-2.83910.189421850.1894218599
2.8391-2.95280.184621600.1846216099
2.9528-3.08720.189721850.1897218599
3.0872-3.250.168921700.16892170100
3.25-3.45360.167621630.1676216399
3.4536-3.72020.157821940.15782194100
3.7202-4.09460.149821840.14982184100
4.0946-4.6870.146821990.1468219999
4.687-5.90480.16522000.165220099
5.9048-75.5670.193122660.1931226699
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)
1-0.0002-0.0119-0.01440.1124-0.04740.1131-0.0458-0.032-0.0169-0.03730.0907-0.05490.1231-0.03610.00430.14140.008-0.02320.0981-0.01050.1634-28.718-36.6349-9.7593
20.0544-0.0222-0.01660.00830.00710.00440.1523-0.0363-0.0432-0.12380.05570.1024-0.0825-0.07560.09820.2976-0.0585-0.0779-0.11620.24170.2273-11.024-25.7544-4.6708
30.00790.03260.02240.11640.01540.04070.0486-0.0208-0.2659-0.04180.0572-0.01650.0111-0.0322-0.0050.11260.0189-0.01580.099-0.00940.1493-29.8812-31.0611-13.954
40.03660.0085-0.01460.06720.02230.06570.06270.1119-0.207-0.18540.1497-0.09460.31050.3730.00030.27550.0347-0.02580.1846-0.05530.2383-25.1106-37.6275-21.6959
50.01750.0271-0.03790.2008-0.09870.0662-0.0443-0.084-0.1032-0.16870.0168-0.11920.17080.20210.01010.11170.0390.03110.1655-0.02270.1591-26.5857-26.4521-20.7691
60.16560.1259-0.04580.1235-0.10920.1414-0.14390.13750.1329-0.03370.10640.04880.05430.0988-0.00830.10620.01770.01060.12470.00610.0774-27.518-19.2156-24.9583
70.20890.1196-0.10380.1331-0.02870.1250.0247-0.004-0.06270.0047-0.0099-0.0010.02760.01010.0230.0580.0027-0.00340.08110.01460.1012-32.1849-25.2328-7.0956
80.015-0.0028-0.01440.0114-0.00310.0093-0.0562-0.0299-0.07470.1556-0.1368-0.0353-0.05860.0548-0.01640.12840.0128-0.05340.18540.02370.1694-21.8702-26.44584.738
90.0305-0.02940.1090.0226-0.06840.1479-0.0066-0.1082-0.00180.01740.0042-0.009-0.0441-0.0876-0.00020.08270.01380.00530.0956-0.00160.1092-32.1844-19.5305-1.2549
100.00980.02170.02920.12040.02710.03970.0385-0.19450.0386-0.1884-0.19320.0983-0.038-0.2958-0.01090.09040.0260.01730.1772-0.00730.1697-26.4338-15.94398.7492
110.10650.03240.04990.0571-0.02610.11170.0537-0.3542-0.34490.07040.06460.00980.1815-0.10160.07860.1093-0.027-0.010.19560.06050.1192-4.6288-19.555819.4536
120.06540.01290.0959-0.01710.00180.13710.0082-0.2087-0.0318-0.01590.0233-0.04350.01290.00810.0050.0835-0.0050.00530.1066-0.00090.126-4.2077-17.42978.4219
130.14650.01940.01960.00530.03740.05460.01770.0450.291-0.09450.0138-0.0287-0.0602-0.0483-0.04560.10350.00530.03010.07320.05620.1394-12.8244-9.84665.944
140.0554-0.0224-0.03390.1109-0.03030.0510.024-0.18780.1708-0.0886-0.047-0.0443-0.0751-0.0183-0.02510.1346-0.00960.00150.1036-0.0220.14371.717-7.853413.4487
150.16270.2785-0.24360.5088-0.35580.6302-0.091-0.32620.09480.2033-0.2567-0.276-0.1150.0307-0.38980.14550.0111-0.00540.3217-0.1308-0.0339-2.8336-12.478426.8869
160.3228-0.09770.0990.0698-0.04890.0217-0.1749-0.13060.154-0.1070.0690.0442-0.0947-0.0170.00770.2289-0.01960.00320.09610.01420.1321-5.4402-30.736229.8973
170.00930.0044-0.00480.0030.0010.0036-0.0724-0.005-0.13780.09130.0563-0.0599-0.1509-0.1282-00.31550.0838-0.020.16480.00430.2215-1.2991-41.533711.8881
180.0450.0094-0.00670.10880.02150.00510.067-0.06180.0542-0.01950.01320.0454-0.1163-0.123200.1949-0.01760.01570.12640.00950.1264-2.3-36.298332.914
190.2650.03980.18660.03140.05840.2092-0.25530.12630.23410.08630.06-0.104-0.16510.1672-0.01350.2438-0.042-0.0410.11550.00550.21526.7625-29.766532.4985
200.0604-0.0193-0.04340.1189-0.05420.05690.0440.28190.1898-0.00460.0816-0.0553-0.1044-0.0066-0.01350.145-0.00870.03160.19360.0040.1215.238-40.919833.3137
210.1543-0.10430.06990.10170.02580.0777-0.09470.02480.05520.02660.2507-0.02290.16190.13030.10420.1152-0.0096-0.02810.15190.04070.10728.4539-48.179836.1167
220.1535-0.0171-0.05260.15820.10170.10410.0354-0.00650.008-0.04890.02580.0379-0.0634-0.08130.04450.1360.0210.01250.11710.04120.0953-9.4426-42.084431.6126
230.01040.0053-0.00710.0158-0.00410.00360.0931-0.0594-0.0209-0.0629-0.1019-0.0382-0.1352-0.0316-00.1733-0.0284-0.0070.20480.03460.1083-14.7989-40.772316.8399
240.04570.02070.05160.03490.00370.11220.05190.01790.00160.0143-0.0565-0.02610.0307-0.22-0.00610.1388-0.02950.00750.13610.03470.1063-14.6983-47.705228.8279
250.03790.0160.06210.50690.12380.10330.0205-0.0674-0.01910.2581-0.0826-0.0970.126-0.23360.01030.0955-0.0060.03650.20130.04470.1239-20.6725-51.231818.8396
260.1758-0.0960.010.13010.0580.14070.08110.15280.1434-0.09510.0493-0.0097-0.4385-0.52250.06010.12660.05920.00050.30090.02210.1183-19.2464-47.7008-5.4483
270.0890.07410.09520.07850.02840.11610.03570.1005-0.0127-0.00110.0553-0.0369-0.0498-0.16830.00320.15020.0076-0.00120.1310.01170.1175-9.4245-49.8492-0.398
280.01720.0177-0.01280.00910.00230.0348-0.046-0.0215-0.06320.03120.067-0.09050.2466-0.1569-0.00270.1792-0.0077-0.00770.11480.04070.1659-11.5104-57.4268.3722
290.03810.021-0.03080.0531-0.02260.0216-0.00720.0523-0.148-0.0262-0.0198-0.08180.185-0.11580.01430.1521-0.0203-0.01630.09350.00270.1372-10.9207-59.4415-7.995
300.6159-0.489-0.30030.62240.46560.45420.3760.0268-0.321-0.4949-0.13960.11410.0635-0.36380.2183-0.0979-0.1194-0.06350.39790.00150.1454-24.8865-54.7784-10.5941
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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