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- PDB-6kod: Cu(II) complex of HOCl-induced flavoprotein disulfide reductase R... -

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Basic information

Entry
Database: PDB / ID: 6kod
TitleCu(II) complex of HOCl-induced flavoprotein disulfide reductase RclA C43S mutant from Escherichia coli
ComponentsPyridine nucleotide-disulphide oxidoreductase dimerisation region
KeywordsOXIDOREDUCTASE / Flavoprotein / hypochlorous acid / reductase / cysteine disulfide / copper / cupric ion
Function / homology
Function and homology information


response to hypochlorite / oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor / cupric reductase (NADH) activity / NAD(P)H dehydrogenase (quinone) activity / 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
COPPER (II) ION / 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: 3 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
DepositionAug 9, 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 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 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)202,56561
Polymers196,0834
Non-polymers6,48257
Water00
1
A: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
B: Pyridine nucleotide-disulphide oxidoreductase dimerisation region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,36432
Polymers98,0422
Non-polymers3,32230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-229 kcal/mol
Surface area34590 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)101,20129
Polymers98,0422
Non-polymers3,16027
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-213 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.498, 189.261, 94.933
Angle α, β, γ (deg.)90.000, 107.434, 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: 49020.754 Da / Num. of mol.: 4 / Mutation: C43S
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: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Ammonium sulfate, 0.05 M Bis-Tris HCl (pH 5.8), 28 % pentaerythrytol ethoxylate (15/4_EO/OH), 5 mM CuSO4

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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: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 45601 / % possible obs: 92.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 51.4 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.045 / Rrim(I) all: 0.098 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2029 / CC1/2: 0.669 / Rpim(I) all: 0.163 / Rrim(I) all: 0.288

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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: 6KGY

6kgy


Resolution: 3→46.61 Å / SU ML: 0.3745 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 25.1906
RfactorNum. reflection% reflection
Rfree0.2565 2022 4.47 %
Rwork0.2081 --
obs0.2103 45241 91.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.72 Å2
Refinement stepCycle: LAST / Resolution: 3→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13547 0 265 0 13812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002614052
X-RAY DIFFRACTIONf_angle_d0.516819115
X-RAY DIFFRACTIONf_chiral_restr0.04372211
X-RAY DIFFRACTIONf_plane_restr0.00282476
X-RAY DIFFRACTIONf_dihedral_angle_d7.859310758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.060.3261120.25922362X-RAY DIFFRACTION70.16
3.06-3.150.30191400.25192775X-RAY DIFFRACTION82.7
3.15-3.240.34491220.2492896X-RAY DIFFRACTION86.77
3.24-3.340.2791440.23032968X-RAY DIFFRACTION89.3
3.34-3.460.32541480.22443011X-RAY DIFFRACTION88.99
3.46-3.60.2891300.21293072X-RAY DIFFRACTION91.33
3.6-3.770.26641450.20943094X-RAY DIFFRACTION91.99
3.77-3.960.24351470.20653166X-RAY DIFFRACTION94.5
3.96-4.210.2451520.18933246X-RAY DIFFRACTION96.56
4.21-4.540.22591520.18263303X-RAY DIFFRACTION97.27
4.54-4.990.23841570.17473274X-RAY DIFFRACTION98.25
4.99-5.710.23151500.20793318X-RAY DIFFRACTION98.13
5.71-7.190.25571630.22533338X-RAY DIFFRACTION98.43
7.19-46.610.22061600.20253396X-RAY DIFFRACTION99.64

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