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- PDB-4c14: The crystal strucuture of PpAzoR in complex with reactive black 5... -

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Basic information

Entry
Database: PDB / ID: 4c14
TitleThe crystal strucuture of PpAzoR in complex with reactive black 5 (RB5)
ComponentsFMN-DEPENDENT NADH-AZOREDUCTASE 1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / FMN-dependent NADH-azoreductase / oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / electron transfer activity
Similarity search - Function
NADH:quinone oxidoreductase, FMN-dependent / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FD5 / FMN-dependent NADH:quinone oxidoreductase 1
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGoncalves, A.M.D. / de Sanctis, D. / Bento, I.
CitationJournal: FEBS J. / Year: 2013
Title: The crystal structure of Pseudomonas putida azoreductase - the active site revisited.
Authors: Goncalves, A.M. / Mendes, S. / de Sanctis, D. / Martins, L.O. / Bento, I.
History
DepositionAug 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Atomic model
Revision 1.2Dec 18, 2013Group: Database references
Revision 2.0Jan 30, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: FMN-DEPENDENT NADH-AZOREDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1133
Polymers21,3861
Non-polymers1,7272
Water2,558142
1
A: FMN-DEPENDENT NADH-AZOREDUCTASE 1
hetero molecules

A: FMN-DEPENDENT NADH-AZOREDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2266
Polymers42,7722
Non-polymers3,4544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area6240 Å2
ΔGint-39.5 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.674, 94.971, 146.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-2093-

HOH

21A-2136-

HOH

31A-2142-

HOH

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Components

#1: Protein FMN-DEPENDENT NADH-AZOREDUCTASE 1 / AZO-DYE REDUCTASE 1 / FMN-DEPENDENT NADH-AZO COMPOUND OXIDOREDUCTASE 1 / AZOREDUCTASE / NAD(P)H ...AZO-DYE REDUCTASE 1 / FMN-DEPENDENT NADH-AZO COMPOUND OXIDOREDUCTASE 1 / AZOREDUCTASE / NAD(P)H QUINONE OXIDOREDUCTASE


Mass: 21386.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FMN-BINDING PROTEIN / Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: MET94 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER
References: UniProt: Q88IY3, Oxidoreductases; Acting on other nitrogenous compounds as donors, NAD(P)H dehydrogenase (quinone)
#2: Chemical ChemComp-FD5 / [5-[3-[2-[[4-[2-[1-azanyl-7-[2-[4-[methyl-bis(oxidanyl)-$l^{4}-sulfanyl]phenyl]hydrazinyl]-8-oxidanyl-3,6-bis[tris(oxidanyl)-$l^{4}-sulfanyl]naphthalen-2-yl]hydrazinyl]phenyl]-bis(oxidanyl)-$l^{4}-sulfanyl]ethoxy]-7,8-dimethyl-2,4-bis(oxidanylidene)benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate / FAD DERIVATIVE


Mass: 1180.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H54N9O21PS4
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.5 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 1.9→73.5 Å / Num. obs: 20109 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 30.004 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C0W

4c0w


Resolution: 1.9→36.337 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1026 5.1 %
Rwork0.1848 --
obs0.1862 20092 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.541 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1493 0 84 142 1719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051667
X-RAY DIFFRACTIONf_angle_d1.6872296
X-RAY DIFFRACTIONf_dihedral_angle_d21.687619
X-RAY DIFFRACTIONf_chiral_restr0.054245
X-RAY DIFFRACTIONf_plane_restr0.004287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.30541460.23882700X-RAY DIFFRACTION100
2.0002-2.12550.29881110.22562729X-RAY DIFFRACTION100
2.1255-2.28960.27411600.21622690X-RAY DIFFRACTION100
2.2896-2.51990.22631630.19912675X-RAY DIFFRACTION99
2.5199-2.88440.23081600.18992675X-RAY DIFFRACTION98
2.8844-3.63350.21531380.18322746X-RAY DIFFRACTION99
3.6335-36.34370.17091480.16352851X-RAY DIFFRACTION100

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