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

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Basic information

Entry
Database: PDB / ID: 8sbx
TitleCrystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (Apo, hexagonal form)
Components2,3-dihydroxybenzoate-2,3-dehydrogenase
KeywordsOXIDOREDUCTASE / 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-dihydroxybenzoate-2,3-dehydrogenase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle 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)HHSN272201700059C 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 (Apo, hexagonal form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionApr 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)56,27415
Polymers55,1462
Non-polymers1,12813
Water73941
1
A: 2,3-dihydroxybenzoate-2,3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0897
Polymers27,5731
Non-polymers5166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2,3-dihydroxybenzoate-2,3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1858
Polymers27,5731
Non-polymers6127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.845, 125.845, 105.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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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)
Strain: ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M Ammonium Sulfate, 0.1 M Hepes pH 7.0. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate: liu-S-077 well G9, Puck: PSL-0611, Cryo: 2.5 M lithium sulfate

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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, 2022
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: 2.1→108.98 Å / Num. obs: 29313 / % possible obs: 100 % / Redundancy: 39.9 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.012 / Rrim(I) all: 0.076 / Χ2: 1 / Net I/σ(I): 29.3 / Num. measured all: 1168865
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 100 % / Redundancy: 42.6 % / Rmerge(I) obs: 2.395 / Num. measured all: 90066 / Num. unique obs: 2116 / CC1/2: 0.873 / Rpim(I) all: 0.368 / Rrim(I) all: 2.423 / Χ2: 1 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4918: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30.15 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 1401 4.79 %
Rwork0.1916 --
obs0.1941 29233 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 57 41 3741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123757
X-RAY DIFFRACTIONf_angle_d1.0275109
X-RAY DIFFRACTIONf_dihedral_angle_d14.4271289
X-RAY DIFFRACTIONf_chiral_restr0.053585
X-RAY DIFFRACTIONf_plane_restr0.01672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.37831380.34662708X-RAY DIFFRACTION100
2.18-2.260.27341470.26632721X-RAY DIFFRACTION100
2.26-2.360.28391390.23492729X-RAY DIFFRACTION100
2.37-2.490.28971570.23512724X-RAY DIFFRACTION100
2.49-2.650.32231410.24062752X-RAY DIFFRACTION100
2.65-2.850.32371380.23452756X-RAY DIFFRACTION100
2.85-3.140.27511260.23112788X-RAY DIFFRACTION100
3.14-3.590.23861270.20812810X-RAY DIFFRACTION100
3.59-4.520.21061440.15732836X-RAY DIFFRACTION100
4.52-30.150.22211440.1623008X-RAY DIFFRACTION100
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)
10.6176-0.3883-0.17571.66460.32390.86090.132-0.07660.33080.2294-0.25660.24670.0643-0.1677-00.5513-0.10670.05970.546-0.15840.7257-12.827957.585514.5251
20.8750.2818-0.1250.87920.2102-0.06020.23960.03050.43090.2242-0.3219-0.13790.00840.0820.00010.6065-0.0741-0.01470.513-0.06650.71194.061155.196110.8619
30.45960.610.22020.919-0.15910.62260.1413-0.1484-0.14940.1715-0.19550.3730.0781-0.22410.00010.7798-0.1357-0.00510.6132-0.02020.5228-13.564518.040216.939
40.0977-0.0601-0.23750.59260.33530.02220.319-0.14530.03740.2499-0.32220.48010.1295-0.294100.6687-0.17940.040.5928-0.0690.5997-13.991229.622714.8364
50.58210.3918-0.70271.411-0.06560.57060.3556-0.15920.11990.213-0.27360.33340.0317-0.11420.00010.7101-0.13540.00520.5689-0.0840.5114-8.345933.747314.7044
60.1395-0.106-0.2580.32910.41010.531-0.1905-0.1267-0.39030.1840.13860.3351-0.7263-0.22660.00010.6324-0.0123-0.08080.59110.04620.6064-14.412327.66463.8934
70.07010.0269-0.05270.01080.02810.1918-0.36730.01-0.06-0.62650.22090.49890.0462-0.86110.00020.8507-0.0107-0.16151.0086-0.0990.8175-23.61435.4101-9.4357
80.63520.6242-0.06240.5111-0.09840.09280.2832-0.15790.0741-0.1851-0.22560.090.1908-0.062-0.00020.66010.0042-0.07430.5618-0.09670.5156-6.562127.0777-0.9798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 168 )
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 251 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 70 )
4X-RAY DIFFRACTION4chain 'B' and (resid 71 through 95 )
5X-RAY DIFFRACTION5chain 'B' and (resid 96 through 168 )
6X-RAY DIFFRACTION6chain 'B' and (resid 169 through 189 )
7X-RAY DIFFRACTION7chain 'B' and (resid 190 through 205 )
8X-RAY DIFFRACTION8chain 'B' and (resid 206 through 251 )

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