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- PDB-9nrq: GloR with glyoxal modification -

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Basic information

Entry
Database: PDB / ID: 9nrq
TitleGloR with glyoxal modification
ComponentsLysR family transcriptional regulator
KeywordsCYTOSOLIC PROTEIN / glyoxal
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
LysR family transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsCuthbert, B.J. / de Miranda, R. / Martinez, J. / Goulding, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: A glyoxal-specific transcription factor
Authors: Corcoran, C.P. / Cuthbert, B.J. / Glanville, D.G. / de Miranda, R. / Martinez, J. / Goulding, C.W. / Ulijasz, A.T.
History
DepositionMar 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysR family transcriptional regulator
B: LysR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)44,7952
Polymers44,7952
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-12 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.482, 119.111, 34.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein LysR family transcriptional regulator


Mass: 22397.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: DT376_05080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A367MEI0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NaNO3, 0.1 M BisTris Propane pH 8.5, 22.5% PEG 3350
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→38.4 Å / Num. obs: 24888 / % possible obs: 98.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 36.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.053 / Rrim(I) all: 0.164 / Χ2: 0.8 / Net I/σ(I): 6.2
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.284 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1854 / CC1/2: 0.819 / Rpim(I) all: 0.655 / Rrim(I) all: 1.448 / Χ2: 0.64 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→38.4 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 2470 9.99 %
Rwork0.2192 --
obs0.2222 24732 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 0 132 3228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093192
X-RAY DIFFRACTIONf_angle_d1.0654346
X-RAY DIFFRACTIONf_dihedral_angle_d15.4981188
X-RAY DIFFRACTIONf_chiral_restr0.057480
X-RAY DIFFRACTIONf_plane_restr0.011576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.130.38661200.33271082X-RAY DIFFRACTION87
2.13-2.180.32981340.31051205X-RAY DIFFRACTION99
2.18-2.220.32171360.29531217X-RAY DIFFRACTION100
2.22-2.280.32981380.31061244X-RAY DIFFRACTION99
2.28-2.330.33951350.27611219X-RAY DIFFRACTION99
2.33-2.40.31091360.26961233X-RAY DIFFRACTION99
2.4-2.470.31281350.25961222X-RAY DIFFRACTION99
2.47-2.550.28751340.24861207X-RAY DIFFRACTION99
2.55-2.640.32361410.25291259X-RAY DIFFRACTION99
2.64-2.740.30371340.23761216X-RAY DIFFRACTION100
2.74-2.870.2641420.25531268X-RAY DIFFRACTION100
2.87-3.020.30751350.25371220X-RAY DIFFRACTION100
3.02-3.210.25041380.24371248X-RAY DIFFRACTION99
3.21-3.450.21511400.21241265X-RAY DIFFRACTION99
3.45-3.80.22191400.21231250X-RAY DIFFRACTION98
3.8-4.350.21281400.17711258X-RAY DIFFRACTION99
4.35-5.480.18231430.16221293X-RAY DIFFRACTION100
5.48-38.40.22051490.1841356X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.38260.2322-1.62574.93851.0264.68410.00110.01530.2624-0.1027-0.12710.1096-0.26610.21390.11640.1629-0.0212-0.03230.2370.01890.2054-6.896140.3119-17.2833
25.64443.2535-0.92573.9526-1.1661.03270.2369-0.6307-0.8460.2019-0.2648-0.41590.30120.19520.01430.34070.0345-0.06970.34530.05670.3632-7.056917.338-9.9767
31.9091-0.6979-0.16854.72061.54741.38670.07220.17480.1086-0.2508-0.0704-0.4675-0.31260.13540.04450.268-0.03410.02780.3587-0.01450.27752.424341.9662-18.5503
44.6474-0.09360.32794.3087-1.21582.8499-0.0168-0.1577-0.35240.1056-0.01390.03910.05720.11220.04950.216-0.0243-0.01720.2574-0.00610.248-25.151917.1505-13.4222
55.2470.75120.9884.9607-1.16744.0307-0.07030.79370.2032-0.54050.0051-0.09130.01950.05550.08180.2889-0.0124-0.00570.38850.04260.2947-28.127124.1794-25.9148
63.35320.0357-0.34841.99180.4762.0471-0.00390.2876-0.0811-0.3787-0.1350.3802-0.1955-0.2724-0.08650.3228-0.0365-0.09430.3191-0.02460.3175-38.08926.3976-19.92
74.09150.8396-0.8551.9185-1.18780.70560.3426-0.58631.12330.3088-0.19390.1899-0.4401-0.1622-0.1430.4218-0.03440.09480.4233-0.16530.514-24.392247.2225-8.6526
84.2883-1.0544-2.30412.11252.23355.4625-0.06150.62921.22-0.4808-0.01841.7849-0.1957-1.0780.1230.48990.08730.05580.4526-0.01930.7438-31.26346.967-16.3933
93.7910.63040.25351.6790.032.3990.1699-0.35820.65520.1284-0.28220.3601-0.24890.00890.04090.3155-0.04460.0380.3093-0.0740.3724-19.917444.0537-8.8832
103.14570.89522.5991.9360.47243.82690.1099-1.27720.32870.5156-0.08850.1257-0.2-0.5890.07080.41230.00560.0710.6638-0.10060.3625-25.702940.2895-1.0048
112.7738-0.45170.25484.6015-2.15021.81770.15260.3183-0.2604-0.2862-0.09420.52220.35710.1539-0.06590.28520.0286-0.02850.3579-0.03090.3382-35.547517.4115-18.7458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 86 through 145 )
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 258 )
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 283 )
4X-RAY DIFFRACTION4chain 'B' and (resid 87 through 126 )
5X-RAY DIFFRACTION5chain 'B' and (resid 127 through 145 )
6X-RAY DIFFRACTION6chain 'B' and (resid 146 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 193 )
8X-RAY DIFFRACTION8chain 'B' and (resid 194 through 204 )
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 239 )
10X-RAY DIFFRACTION10chain 'B' and (resid 240 through 258 )
11X-RAY DIFFRACTION11chain 'B' and (resid 259 through 283 )

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