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- PDB-7q6m: Structure of WrbA from Yersinia pseudotuberculosis in P1 -

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Basic information

Entry
Database: PDB / ID: 7q6m
TitleStructure of WrbA from Yersinia pseudotuberculosis in P1
ComponentsNAD(P)H dehydrogenase (quinone)
KeywordsFLAVOPROTEIN / NADH dehydrogenase / oxidoreductase
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
NAD(P)H dehydrogenase (quinone), prokaryotic / Flavoprotein WrbA-like / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily
Similarity search - Domain/homology
NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsGabrielsen, M. / Beckham, K.S.H. / Roe, A.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Microbiology (Reading, Engl.) / Year: 2022
Title: Crystal structures of WrbA, a spurious target of the salicylidene acylhydrazide inhibitors of type III secretion in Gram-negative pathogens, and verification of improved specificity of next-generation compounds.
Authors: Zambelloni, R. / Beckham, K.S.H. / Wu, H.J. / Elofsson, M. / Marquez, R. / Gabrielsen, M. / Roe, A.J.
History
DepositionNov 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)
C: NAD(P)H dehydrogenase (quinone)
D: NAD(P)H dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6258
Polymers98,4834
Non-polymers1424
Water9,476526
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Established in literature
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.690, 63.860, 66.360
Angle α, β, γ (deg.)61.210, 77.900, 86.930
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain A and (resid 1 through 49 or (resid 50...
d_2ens_1(chain B and (resid 1 through 55 or (resid 56...
d_3ens_1(chain C and (resid 1 through 49 or (resid 50...
d_4ens_1(chain D and (resid 1 through 57 or (resid 58...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETALAALA(chain A and (resid 1 through 49 or (resid 50...AA1 - 4934 - 82
d_12LYSLYSALAALA(chain A and (resid 1 through 49 or (resid 50...AA50 - 5183 - 84
d_13METMETLYSLYS(chain A and (resid 1 through 49 or (resid 50...AA1 - 19834 - 231
d_14METMETLYSLYS(chain A and (resid 1 through 49 or (resid 50...AA1 - 19834 - 231
d_15METMETLYSLYS(chain A and (resid 1 through 49 or (resid 50...AA1 - 19834 - 231
d_16METMETLYSLYS(chain A and (resid 1 through 49 or (resid 50...AA1 - 19834 - 231
d_21METMETTHRTHR(chain B and (resid 1 through 55 or (resid 56...BB1 - 5534 - 88
d_22ASNASNASNASN(chain B and (resid 1 through 55 or (resid 56...BB5689
d_23PHEPHELYSLYS(chain B and (resid 1 through 55 or (resid 56...BB-7 - 19826 - 231
d_24PHEPHELYSLYS(chain B and (resid 1 through 55 or (resid 56...BB-7 - 19826 - 231
d_25PHEPHELYSLYS(chain B and (resid 1 through 55 or (resid 56...BB-7 - 19826 - 231
d_26PHEPHELYSLYS(chain B and (resid 1 through 55 or (resid 56...BB-7 - 19826 - 231
d_31METMETALAALA(chain C and (resid 1 through 49 or (resid 50...CC1 - 4934 - 82
d_32LYSLYSALAALA(chain C and (resid 1 through 49 or (resid 50...CC50 - 5183 - 84
d_33METMETLYSLYS(chain C and (resid 1 through 49 or (resid 50...CC1 - 19834 - 231
d_34METMETLYSLYS(chain C and (resid 1 through 49 or (resid 50...CC1 - 19834 - 231
d_35METMETLYSLYS(chain C and (resid 1 through 49 or (resid 50...CC1 - 19834 - 231
d_36METMETLYSLYS(chain C and (resid 1 through 49 or (resid 50...CC1 - 19834 - 231
d_41METMETGLNGLN(chain D and (resid 1 through 57 or (resid 58...DD1 - 5734 - 90
d_42GLNGLNALAALA(chain D and (resid 1 through 57 or (resid 58...DD58 - 5991 - 92
d_43PHEPHELYSLYS(chain D and (resid 1 through 57 or (resid 58...DD-7 - 19826 - 231
d_44PHEPHELYSLYS(chain D and (resid 1 through 57 or (resid 58...DD-7 - 19826 - 231
d_45PHEPHELYSLYS(chain D and (resid 1 through 57 or (resid 58...DD-7 - 19826 - 231
d_46PHEPHELYSLYS(chain D and (resid 1 through 57 or (resid 58...DD-7 - 19826 - 231

NCS oper:
IDCodeMatrixVector
1given(0.58317097351, -0.0796081878934, -0.808439331104), (-0.086913398096, -0.995588782111, 0.0353417340706), (-0.807686620471, 0.0496539359573, -0.587517497405)3.88819525453, 60.2650693081, 1.32441290259
2given(-0.994280682894, 0.106792269617, -0.0011553241052), (0.106790095949, 0.994279952532, 0.00180316390945), (0.00134127956286, 0.00166947387121, -0.99999770691)-24.9242654761, 1.30474644246, 14.6065433818
3given(-0.588446251079, -0.0263145184666, 0.808108009927), (-0.024332962001, -0.998441157758, -0.0502310805637), (0.808170103722, -0.0492219525437, 0.586888646028)-22.3972225431, 61.6680478451, 13.2974906573

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Components

#1: Protein
NAD(P)H dehydrogenase (quinone) / Flavoprotein WrbA / NAD(P)H:quinone oxidoreductase / NQO


Mass: 24620.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: YPTB1728 / Production host: Escherichia coli (E. coli)
References: UniProt: Q66BP3, NAD(P)H dehydrogenase (quinone)
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.01 M nickel chloride hexahydrate, 0.1 M Tris pH 8.5, 20 % w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.03→46.17 Å / Num. obs: 123249 / % possible obs: 91.4 % / Observed criterion σ(F): 1.98 / Redundancy: 2.5 % / Biso Wilson estimate: 11.83 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.051 / Rrim(I) all: 0.079 / Net I/σ(I): 1.17
Reflection shellResolution: 2.03→2.09 Å / Mean I/σ(I) obs: 1.72 / Num. unique obs: 2434 / CC1/2: 0.951 / Rpim(I) all: 0.109 / Rrim(I) all: 0.154 / % possible all: 59.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R96

2r96


Resolution: 2.04→43.86 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 5014 5.07 %
Rwork0.1736 93828 -
obs0.1756 98842 91.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.41 Å2 / Biso mean: 14.0114 Å2 / Biso min: 4.44 Å2
Refinement stepCycle: final / Resolution: 2.04→43.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5921 0 4 526 6451
Biso mean--30.24 21.69 -
Num. residues----808
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
ens_11A2340X-RAY DIFFRACTION3.74TORSIONAL
ens_12B2340X-RAY DIFFRACTION3.74TORSIONAL
ens_13C2340X-RAY DIFFRACTION3.74TORSIONAL
ens_14D2340X-RAY DIFFRACTION3.74TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.070.2391060.21262085219160
2.07-2.090.25941440.19163065320990
2.09-2.120.19951160.18363041315790
2.12-2.140.22492090.17823081329089
2.14-2.170.22691640.18253030319490
2.17-2.20.21491780.18163125330390
2.2-2.230.17141520.17453047319990
2.23-2.270.27291700.1743093326391
2.27-2.30.20351540.17633130328491
2.3-2.340.23291510.17963162331392
2.34-2.380.24371730.17673082325591
2.38-2.420.18841600.17273175333592
2.42-2.470.19241560.16263044320091
2.47-2.520.20511500.16313178332893
2.52-2.580.20721750.1653204337992
2.58-2.640.20011360.17233116325292
2.64-2.70.24341540.17233171332593
2.7-2.780.22132120.17393242345493
2.78-2.860.22721440.18233143328793
2.86-2.950.20891810.1873191337294
2.95-3.050.23141840.18493230341494
3.05-3.180.26071830.18183206338994
3.18-3.320.21751850.16773192337794
3.32-3.50.20781650.16913254341995
3.5-3.720.22562030.1693188339195
3.72-40.21871620.15993288345096
4-4.40.1711660.15493261342796
4.4-5.040.16842080.14773249345796
5.04-6.350.18011850.18293271345697
6.35-43.860.21431880.20143284347296
Refinement TLS params.Method: refined / Origin x: -10.8788 Å / Origin y: 30.8181 Å / Origin z: 7.2569 Å
111213212223313233
T0.0481 Å20.0012 Å20.0142 Å2-0.0621 Å2-0.005 Å2--0.0581 Å2
L0.2192 °20.0055 °20.1848 °2-0.4711 °2-0.0142 °2--0.54 °2
S-0.0073 Å °-0.0046 Å °0.0208 Å °0.004 Å °0.0011 Å °-0.0067 Å °-0.0477 Å °0.0055 Å °0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 198
2X-RAY DIFFRACTION1allB-7 - 198
3X-RAY DIFFRACTION1allC1 - 198
4X-RAY DIFFRACTION1allD-7 - 198
5X-RAY DIFFRACTION1allF4 - 148
6X-RAY DIFFRACTION1allE1 - 489
7X-RAY DIFFRACTION1allG1 - 2
8X-RAY DIFFRACTION1allI1
9X-RAY DIFFRACTION1allJ1

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