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- PDB-6kgy: HOCl-induced flavoprotein disulfide reductase RclA from Escherich... -

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Basic information

Entry
Database: PDB / ID: 6kgy
TitleHOCl-induced flavoprotein disulfide reductase RclA from Escherichia coli
ComponentsPyridine nucleotide-disulphide oxidoreductase dimerisation region
KeywordsOXIDOREDUCTASE / Flavoprotein / hypochlorous acid / reductase / cysteine disulfide
Function / homology
Function and homology information


response to hypochlorite / cupric reductase (NADH) activity / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / oxidoreductase activity, acting on NAD(P)H / flavin adenine dinucleotide binding / protein homodimerization activity
Similarity search - Function
Pyridine nucleotide-disulphide oxidoreductase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Pyridine nucleotide-disulphide oxidoreductase dimerisation region / Probable pyridine nucleotide-disulfide oxidoreductase RclA
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBaek, Y. / Ha, N.-C.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure and function of the hypochlorous acid-induced flavoprotein RclA fromEscherichia coli.
Authors: Baek, Y. / Kim, J. / Ahn, J. / Jo, I. / Hong, S. / Ryu, S. / Ha, N.C.
History
DepositionJul 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
B: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
C: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
D: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,39611
Polymers196,1474
Non-polymers3,2497
Water46826
1
A: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
B: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6805
Polymers98,0742
Non-polymers1,6073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-62 kcal/mol
Surface area33600 Å2
MethodPISA
2
C: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
D: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7166
Polymers98,0742
Non-polymers1,6424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-55 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.455, 189.429, 95.422
Angle α, β, γ (deg.)90.000, 107.324, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Pyridine nucleotide-disulphide oxidoreductase dimerisation region / Flavoprotein disulfide reductase


Mass: 49036.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Gene: ECBD_3354 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A140ND83, UniProt: P77212*PLUS
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M Bis-Tris HCl pH 5.8, 13% PEG 3350, 2 mM TCEP

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 54340 / % possible obs: 98.5 % / Redundancy: 5 % / Biso Wilson estimate: 43.62 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.044 / Rrim(I) all: 0.109 / Χ2: 0.708 / Net I/σ(I): 12.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.21 / Num. unique obs: 2560 / CC1/2: 0.778 / Rpim(I) all: 0.144 / Rrim(I) all: 0.287 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: sequence based de novo model (Galaxy Web server)

Resolution: 2.9→40.37 Å / SU ML: 0.4122 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 27.3977
RfactorNum. reflection% reflection
Rfree0.2793 2010 3.72 %
Rwork0.233 --
obs0.2348 54069 96.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.43 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13495 0 215 26 13736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002613994
X-RAY DIFFRACTIONf_angle_d0.529319034
X-RAY DIFFRACTIONf_chiral_restr0.0432204
X-RAY DIFFRACTIONf_plane_restr0.00312463
X-RAY DIFFRACTIONf_dihedral_angle_d8.19829900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.30751000.25952710X-RAY DIFFRACTION70.43
2.94-3.020.35771480.26583611X-RAY DIFFRACTION93.41
3.02-3.110.31451520.24653660X-RAY DIFFRACTION96.09
3.11-3.210.281360.24483736X-RAY DIFFRACTION97.31
3.21-3.320.29141420.25283805X-RAY DIFFRACTION98.36
3.32-3.460.30041490.25333780X-RAY DIFFRACTION98.67
3.46-3.610.31781410.24283851X-RAY DIFFRACTION99.2
3.61-3.80.27981530.22933803X-RAY DIFFRACTION99
3.8-4.040.28281390.21753848X-RAY DIFFRACTION99.55
4.04-4.350.25011420.21533820X-RAY DIFFRACTION99.77
4.35-4.790.27511570.20913865X-RAY DIFFRACTION99.73
4.79-5.480.25231510.22363829X-RAY DIFFRACTION99.62
5.48-6.90.27891460.253865X-RAY DIFFRACTION99.9
6.9-40.370.24641540.22693876X-RAY DIFFRACTION98.85

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