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

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Basic information

Entry
Database: PDB / ID: 8sbw
TitleCrystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (Apo, orthorhombic 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
ACETATE ION / 2,3-dihydroxybenzoate-2,3-dehydrogenase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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, orthorhombic 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)55,5897
Polymers55,1462
Non-polymers4435
Water4,324240
1
A: 2,3-dihydroxybenzoate-2,3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7653
Polymers27,5731
Non-polymers1922
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)27,8244
Polymers27,5731
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.258, 111.331, 57.607
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 0.6 M ammonium sulfate, 0.1M sodium acetate pH 4.4. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate: liu-S-078 well A7, Puck: PSL-0604, 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: 1.75→67.26 Å / Num. obs: 44457 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Χ2: 1.03 / Net I/σ(I): 17.8 / Num. measured all: 590368
Reflection shellResolution: 1.75→1.8 Å / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 1.994 / Num. measured all: 43754 / Num. unique obs: 3234 / CC1/2: 0.773 / Rpim(I) all: 0.559 / Rrim(I) all: 2.072 / Χ2: 1.08 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4918: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→42.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 2229 5.03 %
Rwork0.1698 --
obs0.1711 44352 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 24 240 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093277
X-RAY DIFFRACTIONf_angle_d0.9274463
X-RAY DIFFRACTIONf_dihedral_angle_d13.4731126
X-RAY DIFFRACTIONf_chiral_restr0.056523
X-RAY DIFFRACTIONf_plane_restr0.008588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.33091560.29322595X-RAY DIFFRACTION100
1.79-1.830.33531430.27342563X-RAY DIFFRACTION100
1.83-1.880.23341370.24942615X-RAY DIFFRACTION100
1.88-1.930.24111300.2112610X-RAY DIFFRACTION100
1.93-1.980.24271350.19152598X-RAY DIFFRACTION100
1.98-2.050.25361470.18042582X-RAY DIFFRACTION100
2.05-2.120.20371420.17732614X-RAY DIFFRACTION100
2.12-2.20.18871280.16212609X-RAY DIFFRACTION100
2.2-2.310.20451370.15532623X-RAY DIFFRACTION100
2.31-2.430.20691480.15082608X-RAY DIFFRACTION100
2.43-2.580.18631380.14932630X-RAY DIFFRACTION100
2.58-2.780.16771320.15982646X-RAY DIFFRACTION100
2.78-3.060.21081170.17482680X-RAY DIFFRACTION100
3.06-3.50.18751460.16822642X-RAY DIFFRACTION100
3.5-4.410.14581290.14012719X-RAY DIFFRACTION100
4.41-42.880.19821640.17712789X-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)
10.79180.4883-0.03190.54480.26580.68070.09980.1026-0.3169-0.105-0.04220.18340.0721-0.21410.00020.3073-0.0408-0.01990.28720.00820.37712.1851-24.52815.6911
20.56160.1376-0.15081.0631-0.22770.34690.0073-0.0471-0.0763-0.01660.09790.21320.1029-0.29300.2683-0.0448-0.01660.28770.00950.249217.4641-10.74617.123
30.31050.2143-0.19950.3678-0.01990.17480.03450.1217-0.2714-0.1458-0.1297-0.34880.25440.151-0.00020.30470.012-0.00380.2676-0.01960.303930.8704-16.205710.1981
40.5731-0.25150.420.35870.08120.57070.0574-0.2370.32780.0275-0.10230.192-0.2449-0.29370.00020.3210.07940.01290.3082-0.02630.365312.776924.369114.4986
50.0126-0.0075-0.00220.01040.00360.03210.0839-0.0333-0.1513-0.3999-0.27420.3949-0.0295-0.4358-0.00010.3540.0726-0.01220.5647-0.00340.48082.665116.99435.1376
60.3404-0.2036-0.10770.9790.00030.51250.03650.00740.07550.0030.0560.1674-0.1131-0.272400.24860.01830.0050.30110.01880.263215.82958.696312.4673
70.1251-0.008-0.06760.0246-0.02530.07260.0319-0.04530.21490.08480.0109-0.2121-0.3149-0.19510.00310.29780.0365-0.03650.2379-0.03460.246927.480713.934518.8071
80.1826-0.06790.09220.21640.14170.2030.0409-0.01140.25760.0552-0.1029-0.2526-0.12450.1106-00.3191-0.00080.01890.2498-0.00450.297329.361916.396215.3106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 251 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 58 )
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 70 )
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 168 )
7X-RAY DIFFRACTION7chain 'B' and (resid 169 through 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid 218 through 251 )

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