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- PDB-8u9a: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 8u9a
TitleCrystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (DBH bound)
Components2,3-dihydroxybenzoate-2,3-dehydrogenase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase / 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase activity / siderophore biosynthetic process / nucleotide binding
Similarity search - Function
2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
2,3-DIHYDROXY-BENZOIC ACID / 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (DBH bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionSep 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,3-dihydroxybenzoate-2,3-dehydrogenase
B: 2,3-dihydroxybenzoate-2,3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7158
Polymers55,1462
Non-polymers5696
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-41 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.542, 111.087, 57.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 2,3-dihydroxybenzoate-2,3-dehydrogenase


Mass: 27572.984 Da / Num. of mol.: 2 / Mutation: A2N, A3G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: EAE_13665 / Plasmid: KlaeA.01365.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FXS4
#2: Chemical ChemComp-DBH / 2,3-DIHYDROXY-BENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.2M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 1 month soak in 50 mM SODIUM 2,3-DIHYDROXYLBENZOATE (pH 7.0), KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate liu-s-077 drop C1, Puck: PSL- ...Details: 1.2M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 1 month soak in 50 mM SODIUM 2,3-DIHYDROXYLBENZOATE (pH 7.0), KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate liu-s-077 drop C1, Puck: PSL-1315, Cryo: 2.5M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→111.09 Å / Num. obs: 64070 / % possible obs: 91 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.084 / Χ2: 1.02 / Net I/σ(I): 15.3 / Num. measured all: 864646
Reflection shellResolution: 1.5→1.54 Å / % possible obs: 79.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 2.001 / Num. measured all: 55426 / Num. unique obs: 4087 / CC1/2: 0.629 / Rpim(I) all: 0.551 / Rrim(I) all: 2.077 / Χ2: 1.1 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5057: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→25.04 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1872 3192 4.99 %
Rwork0.161 --
obs0.1623 63949 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→25.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 36 274 3480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083336
X-RAY DIFFRACTIONf_angle_d0.8524543
X-RAY DIFFRACTIONf_dihedral_angle_d12.7411147
X-RAY DIFFRACTIONf_chiral_restr0.057526
X-RAY DIFFRACTIONf_plane_restr0.008604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.34251090.30061895X-RAY DIFFRACTION67
1.52-1.550.28851480.25912795X-RAY DIFFRACTION97
1.55-1.570.2981470.22612800X-RAY DIFFRACTION97
1.57-1.60.26261380.22022791X-RAY DIFFRACTION97
1.6-1.630.25461500.21182811X-RAY DIFFRACTION98
1.63-1.660.24871460.20742802X-RAY DIFFRACTION97
1.66-1.690.22881270.19972835X-RAY DIFFRACTION98
1.69-1.730.22451140.20712120X-RAY DIFFRACTION74
1.73-1.770.22841530.19242825X-RAY DIFFRACTION98
1.77-1.810.24011540.18222835X-RAY DIFFRACTION97
1.81-1.860.19981570.17352815X-RAY DIFFRACTION98
1.86-1.920.2104930.17461626X-RAY DIFFRACTION57
1.92-1.980.21541140.15822293X-RAY DIFFRACTION79
1.98-2.050.18661270.1572857X-RAY DIFFRACTION99
2.05-2.130.19351230.15742361X-RAY DIFFRACTION81
2.13-2.230.18311680.14362842X-RAY DIFFRACTION98
2.23-2.350.15931280.14482461X-RAY DIFFRACTION85
2.35-2.490.15671580.14022904X-RAY DIFFRACTION99
2.49-2.690.1571320.14042604X-RAY DIFFRACTION89
2.69-2.960.19431520.15862920X-RAY DIFFRACTION99
2.96-3.380.1711450.15662969X-RAY DIFFRACTION100
3.38-4.260.14921400.13792493X-RAY DIFFRACTION84
4.26-25.040.19771690.16793103X-RAY DIFFRACTION99
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)
14.4771-1.30330.12553.0862-0.13761.97950.05990.1042-0.2551-0.092-0.05480.12650.1445-0.15130.00890.1972-0.05660.00390.1360.00040.189912.2122-24.660616.3409
20.7986-0.3080.41773.2939-2.31653.66710.0257-0.0287-0.0319-0.02740.05620.08580.0806-0.0915-0.0910.1376-0.0220.00050.1436-0.00720.150616.9302-9.707216.1987
33.00931.1572-1.94553.4353-1.11053.916-0.07010.1921-0.129-0.2059-0.0464-0.1940.2053-0.01080.10460.14810.0181-0.00740.1783-0.01070.22329.8142-16.121911.3492
44.05671.35061.15453.58190.60192.60810.0265-0.21590.30050.0287-0.11040.1534-0.2143-0.23410.02530.180.06770.00950.1418-0.01520.150213.017424.503614.5867
56.56071.9154-0.47217.0203-2.27326.7433-0.11570.6950.0996-0.50540.13230.2874-0.0628-0.9134-0.00770.21750.0831-0.01620.41450.02240.26623.064718.29664.3369
61.36932.3437-2.29528.7767-6.37847.1590.0238-0.00390.07120.27110.18720.3289-0.1125-0.3003-0.30310.15310.04510.01530.2226-0.0050.193511.9377.037618.7855
70.79450.1277-0.34422.5177-1.58242.70670.00040.01640.0426-0.0334-0.0117-0.0403-0.0705-0.01770.01510.15130.00790.01290.14860.00470.171918.8549.13579.1746
84.0611-0.74930.46313.5577-0.27091.3953-0.0561-0.670.11270.683-0.0384-0.2468-0.11540.2940.0670.2449-0.0163-0.02920.2522-0.00610.186327.270514.145819.876
91.5595-0.64020.58183.087-1.1594.60540.0083-0.01190.08750.0479-0.1187-0.1517-0.1560.05830.12210.1237-0.0244-0.00660.1664-0.0010.19729.50216.420515.3431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 168 )
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 251 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 58 )
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 72 )
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 107 )
7X-RAY DIFFRACTION7chain 'B' and (resid 108 through 168 )
8X-RAY DIFFRACTION8chain 'B' and (resid 169 through 217 )
9X-RAY DIFFRACTION9chain 'B' and (resid 218 through 251 )

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