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- PDB-4d02: The crystallographic structure of Flavorubredoxin from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 4d02
TitleThe crystallographic structure of Flavorubredoxin from Escherichia coli
ComponentsANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN
KeywordsELECTRON TRANSPORT / FDP / NITRIC OXIDE / ROO / RUBREDOXIN / FLRD
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. / Flavodoxin domain / Metallo-beta-lactamase superfamily ...Anaerobic nitric oxide reductase flavorubredoxin / Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FLAVIN MONONUCLEOTIDE / OXYGEN ATOM / PHOSPHATE ION / Anaerobic nitric oxide reductase flavorubredoxin
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.755 Å
AuthorsRomao, C.V. / Vicente, J.B. / Bandeiras, T. / Carrondo, M.A. / Teixeira, M. / Frazao, C.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure of Escherichia Coli Flavodiiron Nitric Oxide Reductase.
Authors: Romao, C.V. / Vicente, J.B. / Borges, P.T. / Victor, B.L. / Lamosa, P. / Silva, E. / Bandeiras, T.M. / Soares, C.M. / Carrondo, M.A. / Turner, D. / Teixeira, M. / Frazao, C.
History
DepositionApr 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,32211
Polymers54,2931
Non-polymers1,02910
Water7,620423
1
A: ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN
hetero molecules

A: ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,64422
Polymers108,5862
Non-polymers2,05820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11
Buried area9020 Å2
ΔGint-159.3 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.529, 149.529, 94.498
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-2098-

HOH

21A-2168-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN / FLRD / FLAVORB / FLAVORUBREDOXIN


Mass: 54293.004 Da / Num. of mol.: 1 / Fragment: B-LACTAMASE FLAVODOXIN DOMAIN, RESIDUES 1-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q46877

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Non-polymers , 7 types, 433 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOUR DIFFUSION (HANGING DROP) AT 34C (307 K) USING 1.0UL OF PROTEIN AT14 MG/ML WITH 1 UL OF CRYSTALLIZATION SOLUTION (0.2M NA-CACODYLATE PH 6.5, 0.2 M MGACETATE, 20% PEG8000).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.69841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
Details: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR AND A CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: SI(111) MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.69841 Å / Relative weight: 1
ReflectionResolution: 1.75→129.5 Å / Num. obs: 60074 / % possible obs: 95.5 % / Observed criterion σ(I): 1.64 / Redundancy: 14.2 % / Biso Wilson estimate: 23.03 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 28.4
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.64 / % possible all: 75.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.755→129.496 Å / SU ML: 0.13 / σ(F): 1.25 / Phase error: 15.67 / Stereochemistry target values: LS_WUNIT_K1
Details: THE REFINEMENT CONVERGED TO R- -WORK AND R-FREE OF 0.1444 AND 0.1666, RESPECTIVELY, WITH A R-FREE SET OF 5401 REFLECTIONS. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET. THE ...Details: THE REFINEMENT CONVERGED TO R- -WORK AND R-FREE OF 0.1444 AND 0.1666, RESPECTIVELY, WITH A R-FREE SET OF 5401 REFLECTIONS. THE FINAL MODEL WAS THEN REFINED VERSUS THE FULL DATA SET. THE FOLLOWING AMINOACID RESIDUES WERE MODELED WITH SIDE CHAINS IN DOUBLED CONFORMATION SER56, ARG57, LYS125, THR185, ANS217, , ARG253, VAL290, ARG339, SER357. IT WAS ONLY MODELED THE AMINOACID RESIDUES FROM 2 TO 400, BECAUSE THE RUBREDOXIN DOMAIN AT C-TERMINAL WAS NOT VISIBLE IN THE 2FO-FC MAPS. THE NATURE OF PHOSPHATE AND CHLORIDE SOLVENT MOLECULES WAS CONFIRMED BY THEIR ANOMALOUS SIGNAL.
RfactorNum. reflection% reflection
Rwork0.1407 --
obs0.1407 59089 94.31 %
Rfree-2902 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 1.755→129.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 58 423 3687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153375
X-RAY DIFFRACTIONf_angle_d0.9244563
X-RAY DIFFRACTIONf_dihedral_angle_d13.3851229
X-RAY DIFFRACTIONf_chiral_restr0.034493
X-RAY DIFFRACTIONf_plane_restr0.003586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7545-1.77450.01359910.0135991X-RAY DIFFRACTION25
1.7745-1.79540.396628090.39662809X-RAY DIFFRACTION71
1.7954-1.81730.287830980.28783098X-RAY DIFFRACTION78
1.8173-1.84030.283532990.28353299X-RAY DIFFRACTION83
1.8403-1.86450.269434770.26943477X-RAY DIFFRACTION88
1.8645-1.890.24136310.2413631X-RAY DIFFRACTION92
1.89-1.9170.224437490.22443749X-RAY DIFFRACTION95
1.917-1.94570.203138120.20313812X-RAY DIFFRACTION97
1.9457-1.97610.198839280.19883928X-RAY DIFFRACTION100
1.9761-2.00850.188739440.18873944X-RAY DIFFRACTION100
2.0085-2.04310.185139420.18513942X-RAY DIFFRACTION100
2.0431-2.08020.179339580.17933958X-RAY DIFFRACTION100
2.0802-2.12030.172538800.17253880X-RAY DIFFRACTION100
2.1203-2.16350.166639760.16663976X-RAY DIFFRACTION100
2.1635-2.21060.156139730.15613973X-RAY DIFFRACTION100
2.2106-2.2620.155139360.15513936X-RAY DIFFRACTION100
2.262-2.31860.158139250.15813925X-RAY DIFFRACTION100
2.3186-2.38130.158239270.15823927X-RAY DIFFRACTION100
2.3813-2.45140.154239730.15423973X-RAY DIFFRACTION100
2.4514-2.53050.149239430.14923943X-RAY DIFFRACTION100
2.5305-2.62090.142439330.14243933X-RAY DIFFRACTION100
2.6209-2.72590.147739510.14773951X-RAY DIFFRACTION100
2.7259-2.850.136339240.13633924X-RAY DIFFRACTION100
2.85-3.00020.13139520.1313952X-RAY DIFFRACTION100
3.0002-3.18820.120239380.12023938X-RAY DIFFRACTION100
3.1882-3.43440.109439270.10943927X-RAY DIFFRACTION100
3.4344-3.780.099439800.09943980X-RAY DIFFRACTION100
3.78-4.3270.088839430.08883943X-RAY DIFFRACTION100
4.327-5.45170.095239290.09523929X-RAY DIFFRACTION100
5.4517-129.850.128739730.12873973X-RAY DIFFRACTION99
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)
11.18640.22860.67640.80.63721.59790.18610.221-0.3058-0.2106-0.1047-0.06970.19470.027-0.04680.3110.0586-0.05980.2669-0.06250.292129.460945.58422.932
21.7397-0.7747-0.50714.62730.06610.60450.09140.08330.09490.008-0.04750.08590.12640.0431-0.08260.23630.0233-0.02130.2136-0.03180.237328.427459.6138.2545
30.82620.08850.44760.64630.01042.16550.07430.3184-0.2229-0.3045-0.15380.04730.1852-0.02120.00950.35480.0732-0.05750.3464-0.10540.279124.155248.71916.1365
42.5681-0.3776-0.38122.79371.32454.97920.14560.18220.0073-0.3577-0.1974-0.2317-0.04840.29560.05550.31910.0835-0.00220.3374-0.02290.263334.554154.537116.3871
51.3484-0.3728-0.46620.96810.1371.28510.17850.304-0.0096-0.3978-0.18420.0592-0.0543-0.00210.00880.38860.0961-0.05740.3351-0.03650.238423.20758.862213.3603
61.45060.6431-0.10561.42240.17310.68430.07640.3327-0.0147-0.478-0.1020.2159-0.1878-0.15190.04730.45220.1148-0.09980.3549-0.04680.257716.721762.985612.5239
70.6841-0.0401-0.13570.51790.09230.54010.11590.2072-0.2235-0.2571-0.13010.19710.065-0.02980.02280.29040.0492-0.08750.2674-0.08460.315716.761549.443122.8906
81.3696-1.2908-0.42532.61050.70020.5298-0.09060.0496-0.13440.00040.01960.05830.10770.02280.09420.18650.0124-0.01420.2294-0.02550.273121.721947.724439.2437
91.0981-0.45640.15890.743-0.11140.74290.04330.1346-0.3646-0.1443-0.09860.3910.1132-0.14720.0580.22850.0081-0.05080.2435-0.0820.358811.081247.16129.0359
101.3698-0.9016-0.64130.79631.33394.2793-0.08130.0275-0.41280.0214-0.11330.32430.1353-0.21190.18820.1828-0.01010.00110.241-0.04410.37478.77949.789441.718
111.2292-0.03430.26051.21880.18740.7911-0.0155-0.1842-0.18380.06380.06490.00990.0247-0.0081-0.04310.14940.007-0.00670.20820.02570.193919.610459.654760.4383
120.7104-0.0583-0.0930.48340.09090.57630.0219-0.0122-0.0319-0.0268-0.0067-0.0165-0.0404-0.0068-0.0030.15930.01580.00120.1864-0.00090.183918.375366.457353.0617
132.73932.1073-1.16084.3733-0.58851.8927-0.02030.0182-0.0862-0.0411-0.02920.38310.0598-0.01040.11260.16710.0256-0.01830.2206-0.00380.237211.758965.669544.6435
141.20020.45350.56510.7840.88471.57060.0341-0.1850.0444-0.0196-0.0451-0.0149-0.0638-0.1839-0.00140.14910.01580.0090.21160.00430.200911.513671.464159.3852
152.87831.91411.43842.47271.77462.41290.0992-0.3888-0.080.2018-0.12260.07590.1288-0.1310.00550.21320.00640.02930.30140.04070.251211.227460.279869.0315
163.4147-1.0074-0.42882.45490.03952.41310.2268-0.22380.28460.0229-0.09830.0137-0.02160.0692-0.10310.21510.01610.00620.2469-0.0410.213423.631777.966264.1234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:19)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 20:31)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 32:50)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 51:69)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 70:106)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 107:131)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 132:179)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 180:198)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 199:239)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 240:251)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 252:295)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 296:325)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 326:337)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 338:375)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 376:400)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 482:482)

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