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- PDB-6h0c: Flv1 flavodiiron core from Synechocystis sp. PCC6803 -

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Basic information

Entry
Database: PDB / ID: 6h0c
TitleFlv1 flavodiiron core from Synechocystis sp. PCC6803
ComponentsPutative diflavin flavoprotein A 3
KeywordsOXIDOREDUCTASE / Flavodiiron protein / non-canonical residues / cyanobacteria
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / Oxidoreductases / FMN binding / electron transfer activity
Similarity search - Function
: / ODP domain / ODP family beta lactamase / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Flavodoxin, conserved site / Flavodoxin signature. / FMN-binding split barrel / Flavodoxin domain ...: / ODP domain / ODP family beta lactamase / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Flavodoxin, conserved site / Flavodoxin signature. / FMN-binding split barrel / Flavodoxin domain / 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
CITRATE ANION / Putative diflavin flavoprotein A 3
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.592 Å
AuthorsBorges, P.T. / Romao, C.V. / Saraiva, L. / Goncalves, V.L. / Carrondo, M.A. / Teixeira, M. / Frazao, C.
CitationJournal: J. Struct. Biol. / Year: 2019
Title: Analysis of a new flavodiiron core structural arrangement in Flv1-Delta FlR protein from Synechocystis sp. PCC6803.
Authors: Borges, P.T. / Romao, C.V. / Saraiva, L.M. / Goncalves, V.L. / Carrondo, M.A. / Teixeira, M. / Frazao, C.
History
DepositionJul 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative diflavin flavoprotein A 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7093
Polymers44,4841
Non-polymers2252
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-10 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.878, 87.755, 70.665
Angle α, β, γ (deg.)90.00, 100.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

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Components

#1: Protein Putative diflavin flavoprotein A 3


Mass: 44484.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: dfa3, sll1521 / Production host: Escherichia coli (E. coli) / References: UniProt: P74373, Oxidoreductases
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.6 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1 ul of protein at 15 mg/ml with 1 ul of 0.2 M ammonium acetate, 0.1 M tri-sodium citrate pH 5.6, 23-25% (v/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.59→57.23 Å / Num. obs: 58995 / % possible obs: 95.72 % / Redundancy: 2.6 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.039 / Net I/σ(I): 15.1
Reflection shellResolution: 1.59→1.7 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.592→57.225 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.83
Details: THE REFINEMENT OF FLV1 FLAVODIIRON CORE FROM SYNECHOCYSTIS CONVERGED TO RWORK AND RFREE OF 0.153 AND 0.198, RESPECTIVELY, USING A RFREE TEST SET SIZE OF 1.50% (880 REFLECTIONS). THE FINAL ...Details: THE REFINEMENT OF FLV1 FLAVODIIRON CORE FROM SYNECHOCYSTIS CONVERGED TO RWORK AND RFREE OF 0.153 AND 0.198, RESPECTIVELY, USING A RFREE TEST SET SIZE OF 1.50% (880 REFLECTIONS). THE FINAL MODEL THEN WAS REFINED VERSUS THE FULL DATA, RESULTING A FINAL R VALUE OF 0.148.
RfactorNum. reflection% reflection
Rfree0.148 --
Rwork0.148 --
obs0.148 58995 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.592→57.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 14 344 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063233
X-RAY DIFFRACTIONf_angle_d0.9234396
X-RAY DIFFRACTIONf_dihedral_angle_d13.5171175
X-RAY DIFFRACTIONf_chiral_restr0.034491
X-RAY DIFFRACTIONf_plane_restr0.004578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5916-1.60970.339817460.33981746X-RAY DIFFRACTION85
1.6097-1.62870.316119970.31611997X-RAY DIFFRACTION98
1.6287-1.64850.306420160.30642016X-RAY DIFFRACTION98
1.6485-1.66940.304419950.30441995X-RAY DIFFRACTION97
1.6694-1.69140.296619520.29661952X-RAY DIFFRACTION97
1.6914-1.71450.286920440.28692044X-RAY DIFFRACTION97
1.7145-1.7390.273319290.27331929X-RAY DIFFRACTION97
1.739-1.7650.272419420.27241942X-RAY DIFFRACTION94
1.765-1.79260.25119830.2511983X-RAY DIFFRACTION97
1.7926-1.8220.259220220.25922022X-RAY DIFFRACTION98
1.822-1.85340.263319660.26331966X-RAY DIFFRACTION98
1.8534-1.88710.239920100.23992010X-RAY DIFFRACTION98
1.8871-1.92340.222120040.22212004X-RAY DIFFRACTION97
1.9234-1.96260.218819900.21881990X-RAY DIFFRACTION98
1.9626-2.00530.204119980.20411998X-RAY DIFFRACTION97
2.0053-2.0520.208119780.20811978X-RAY DIFFRACTION96
2.052-2.10330.194419280.19441928X-RAY DIFFRACTION95
2.1033-2.16020.190419610.19041961X-RAY DIFFRACTION95
2.1602-2.22370.183819740.18381974X-RAY DIFFRACTION98
2.2237-2.29550.178619990.17861999X-RAY DIFFRACTION97
2.2955-2.37750.17819950.1781995X-RAY DIFFRACTION97
2.3775-2.47270.168119840.16811984X-RAY DIFFRACTION97
2.4727-2.58530.161819870.16181987X-RAY DIFFRACTION96
2.5853-2.72160.154719050.15471905X-RAY DIFFRACTION93
2.7216-2.89210.145719670.14571967X-RAY DIFFRACTION96
2.8921-3.11540.134820010.13482001X-RAY DIFFRACTION97
3.1154-3.42890.11219940.1121994X-RAY DIFFRACTION96
3.4289-3.92490.097419030.09741903X-RAY DIFFRACTION92
3.9249-4.94460.079319140.07931914X-RAY DIFFRACTION93
4.9446-57.26220.100119110.10011911X-RAY DIFFRACTION90
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)
10.76560.3583-0.10960.3195-0.29270.8245-0.12440.2639-0.0053-0.2330.2749-0.12030.1123-0.0928-00.2662-0.00780.00670.3351-0.02720.207714.578748.319433.3369
20.33730.34040.07180.4593-0.12030.6363-0.07710.18450.04640.02420.2815-0.2569-0.11490.0567-0.00010.22340.01250.02160.2762-0.0470.3220.820258.990939.8857
30.0620.16970.18780.55110.55860.6761-0.025-0.19290.20380.27830.3849-0.30720.06870.38820.02760.21850.02150.01260.35-0.16250.539930.011157.629142.017
40.2529-0.0450.16420.2903-0.25370.2984-0.0207-0.28790.14840.61250.166-0.4772-0.19230.24990.04310.34330.0385-0.12460.3011-0.10660.429327.406857.658553.0316
51.0380.2827-0.11240.9842-0.36870.4363-0.04220.09890.02110.1540.14420.0259-0.0377-0.2215-0.00010.23210.0662-0.0010.2720.00270.21337.757651.570145.5973
60.10460.10170.120.21620.11450.1267-0.00450.08550.00290.11280.05230.06360.0061-0.379800.24710.08670.03540.36010.01380.2252.358252.60950.5642
70.16460.01430.17930.1742-0.03090.18740.0641-0.01240.1475-0.15680.00270.06530.0778-0.2442-0.00010.1760.0129-0.02530.4148-0.00250.267-0.586349.792340.4621
80.4444-0.54390.42180.636-0.58071.2823-0.02750.00150.03920.0268-0.0037-0.05640.1953-0.078500.2414-0.01260.00640.2136-0.01380.244114.990133.069756.3719
90.4875-0.2050.07680.2630.27670.62210.1449-0.020.15690.0291-0.0879-0.16990.72750.0830.01750.35650.03230.01130.23010.01210.28622.209124.944559.6205
100.15750.01990.35860.76940.1051.01380.16810.1637-0.1957-0.2072-0.0715-0.12190.86470.19930.00210.46280.04450.00150.2342-0.03280.296919.982121.864451.8213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 28:60)
2X-RAY DIFFRACTION2(chain A and resid 61:114)
3X-RAY DIFFRACTION3(chain A and resid 115:123)
4X-RAY DIFFRACTION4(chain A and resid 124:154)
5X-RAY DIFFRACTION5(chain A and resid 155:234)
6X-RAY DIFFRACTION6(chain A and resid 235:253)
7X-RAY DIFFRACTION7(chain A and resid 254:268)
8X-RAY DIFFRACTION8(chain A and resid 269:355)
9X-RAY DIFFRACTION9(chain A and resid 356:377)
10X-RAY DIFFRACTION10(chain A and resid 378:428)

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