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- PDB-7q6o: Structure of WrbA from Yersinia pseudotuberculosis in C2221 -

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Basic information

Entry
Database: PDB / ID: 7q6o
TitleStructure of WrbA from Yersinia pseudotuberculosis in C2221
ComponentsNAD(P)H dehydrogenase (quinone)
KeywordsFLAVOPROTEIN / NADH dehydrogenase / oxidoreductase
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD binding / FMN binding / flavin adenine dinucleotide binding / NADP binding / membrane
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: 1.99 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 / pdbx_initial_refinement_model

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3124
Polymers49,2422
Non-polymers712
Water2,414134
1
A: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)
hetero molecules

A: NAD(P)H dehydrogenase (quinone)
B: NAD(P)H dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6258
Polymers98,4834
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area9330 Å2
ΔGint-90 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.170, 109.860, 87.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 55 or (resid 56...
d_2ens_1(chain "B" and (resid 1 through 197 or (resid 198...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METGLYA10 - 125
d_12ens_1GLYPHEA128 - 159
d_13ens_1GLYALAA167 - 176
d_14ens_1ARGLYSA182 - 207
d_21ens_1METLYSB1 - 184

NCS oper: (Code: givenMatrix: (-0.853577901094, 0.0395104713873, 0.519464810564), (0.010382085288, -0.995631812741, 0.0927874224365), (0.520861765796, 0.0845944212587, 0.849439111899)Vector: 11. ...NCS oper: (Code: given
Matrix: (-0.853577901094, 0.0395104713873, 0.519464810564), (0.010382085288, -0.995631812741, 0.0927874224365), (0.520861765796, 0.0845944212587, 0.849439111899)
Vector: 11.4099668331, 47.6179115384, -5.45041344194)

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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.: 2
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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 mM sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5, 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.99→55.01 Å / Num. obs: 58533 / % possible obs: 99.9 % / Observed criterion σ(F): 1.33 / Redundancy: 5.2 % / Biso Wilson estimate: 27.05 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.058 / Rrim(I) all: 0.099 / Net I/σ(I): 12.1
Reflection shellResolution: 1.99→2.04 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2157 / CC1/2: 0.919 / Rpim(I) all: 0.445 / Rrim(I) all: 0.763

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Processing

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

2r96


Resolution: 1.99→55.01 Å / SU ML: 0.1772 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2052 2985 5.1 %
Rwork0.1771 55548 -
obs0.1786 58533 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.65 Å2
Refinement stepCycle: LAST / Resolution: 1.99→55.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 2 136 3002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01222929
X-RAY DIFFRACTIONf_angle_d1.32673976
X-RAY DIFFRACTIONf_chiral_restr0.0664450
X-RAY DIFFRACTIONf_plane_restr0.0083509
X-RAY DIFFRACTIONf_dihedral_angle_d13.5826415
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.886417238302 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.32181430.30382643X-RAY DIFFRACTION99.25
2.02-2.060.28041330.27212669X-RAY DIFFRACTION99.54
2.06-2.090.26891460.25432657X-RAY DIFFRACTION99.54
2.09-2.140.24821380.22912654X-RAY DIFFRACTION99.71
2.14-2.180.29331450.22272676X-RAY DIFFRACTION99.33
2.18-2.230.211210.21312631X-RAY DIFFRACTION99.46
2.23-2.280.22071500.2022625X-RAY DIFFRACTION99.25
2.28-2.330.19671530.18742658X-RAY DIFFRACTION99.26
2.33-2.40.23641650.18292654X-RAY DIFFRACTION99.4
2.4-2.470.23551400.17082634X-RAY DIFFRACTION98.97
2.47-2.550.17321650.16712616X-RAY DIFFRACTION99.29
2.55-2.640.20511050.17332676X-RAY DIFFRACTION99.22
2.64-2.750.21981440.1812659X-RAY DIFFRACTION98.98
2.75-2.870.21411580.16632619X-RAY DIFFRACTION99.14
2.87-3.020.21931250.16252624X-RAY DIFFRACTION98.92
3.02-3.210.21481540.1652622X-RAY DIFFRACTION99.04
3.21-3.460.19031390.14952674X-RAY DIFFRACTION99.19
3.46-3.810.19911240.15442667X-RAY DIFFRACTION99.11
3.81-4.360.17881530.14722634X-RAY DIFFRACTION99.29
4.36-5.490.14471540.15272619X-RAY DIFFRACTION98.16
5.49-55.010.21261300.20292637X-RAY DIFFRACTION98.4
Refinement TLS params.Method: refined / Origin x: 4.65919678538 Å / Origin y: 24.3660928108 Å / Origin z: -9.60311544942 Å
111213212223313233
T0.16250374523 Å20.00312523391598 Å2-0.0168171895359 Å2-0.196992674241 Å2-0.0189794583755 Å2--0.156139321563 Å2
L2.15474127109 °20.238506445635 °2-0.747704342407 °2-1.16772412694 °2-0.344629252386 °2--3.23024972256 °2
S0.008675238638 Å °-0.277358142966 Å °-0.042067237061 Å °0.0396372054151 Å °0.0319764384371 Å °-0.0558870279356 Å °-0.0443961941898 Å °0.291669460633 Å °-0.0308038521367 Å °
Refinement TLS groupSelection details: all

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