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

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Basic information

Entry
Database: PDB / ID: 6kyy
TitleCu(II) complex of HOCl-induced flavoprotein disulfide reductase RclA 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: 2.8 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
DepositionSep 20, 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)201,39442
Polymers196,1474
Non-polymers5,24738
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)100,69721
Polymers98,0742
Non-polymers2,62319
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-167 kcal/mol
Surface area34310 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)100,69721
Polymers98,0742
Non-polymers2,62319
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-164 kcal/mol
Surface area34610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.694, 188.955, 95.056
Angle α, β, γ (deg.)90.000, 107.620, 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 mM ammonium sulfate, 0.1 mM Bis-Tris HCl (pH 5.8), 13% PEG 3350, 5 mM CuCl2

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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: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 81985 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 39.02 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Rrim(I) all: 0.081 / Χ2: 0.818 / Net I/σ(I): 17.4
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2849 / CC1/2: 0.826 / Rpim(I) all: 0.198 / Rrim(I) all: 0.369 / Χ2: 0.869 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KGY

6kgy


Resolution: 2.8→47.24 Å / SU ML: 0.3862 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 27.9408
RfactorNum. reflection% reflection
Rfree0.2707 2734 3.33 %
Rwork0.2226 --
obs0.2242 81985 68.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13463 0 246 0 13709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002513928
X-RAY DIFFRACTIONf_angle_d0.519518942
X-RAY DIFFRACTIONf_chiral_restr0.04412198
X-RAY DIFFRACTIONf_plane_restr0.00332448
X-RAY DIFFRACTIONf_dihedral_angle_d9.29498289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.840.3686730.26632362X-RAY DIFFRACTION41.36
2.84-2.890.32161140.26622873X-RAY DIFFRACTION49.27
2.89-2.950.31911140.26362871X-RAY DIFFRACTION49.82
2.95-3.010.3474840.27822925X-RAY DIFFRACTION50.8
3.01-3.070.36281000.27532999X-RAY DIFFRACTION51.32
3.07-3.140.33081140.2633056X-RAY DIFFRACTION52.46
3.14-3.220.30981010.24833070X-RAY DIFFRACTION53.78
3.22-3.310.25351100.24273349X-RAY DIFFRACTION57.23
3.31-3.410.31011140.24383587X-RAY DIFFRACTION61.88
3.41-3.520.24481510.233816X-RAY DIFFRACTION66.13
3.52-3.640.31151380.22743993X-RAY DIFFRACTION68.74
3.64-3.790.25651300.22154238X-RAY DIFFRACTION72.78
3.79-3.960.27391390.2084393X-RAY DIFFRACTION76.42
3.96-4.170.2451730.19874528X-RAY DIFFRACTION78.59
4.17-4.430.23941570.19494663X-RAY DIFFRACTION80.49
4.43-4.770.22831700.19114698X-RAY DIFFRACTION80.32
4.77-5.250.26641670.19794831X-RAY DIFFRACTION83.58
5.25-6.010.28931960.23075506X-RAY DIFFRACTION95.3
6.01-7.570.28631920.23215775X-RAY DIFFRACTION99.93
7.57-47.240.24261970.2235718X-RAY DIFFRACTION98.53

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