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

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Basic information

Entry
Database: PDB / ID: 8sbz
TitleCrystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (NAD bound, No sulfate 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 (NAD bound, No sulfate 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)56,4734
Polymers55,1462
Non-polymers1,3272
Water1,928107
1
A: 2,3-dihydroxybenzoate-2,3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2362
Polymers27,5731
Non-polymers6631
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)28,2362
Polymers27,5731
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.151, 126.151, 104.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-412-

HOH

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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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Berkeley F3: 20% PEG 5000 MME, 0.2 M Ammonium Acetate. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: plate 13163, well F3, drop 2, ...Details: Berkeley F3: 20% PEG 5000 MME, 0.2 M Ammonium Acetate. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: plate 13163, well F3, drop 2, Puck: PSL-0616, Cryo: 20% PEG 200 + 80% crystallant

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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: 1.9→109.25 Å / Num. obs: 38930 / % possible obs: 100 % / Redundancy: 39.5 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.017 / Rrim(I) all: 0.104 / Χ2: 0.99 / Net I/σ(I): 23.4 / Num. measured all: 1537256
Reflection shellResolution: 1.9→1.95 Å / % possible obs: 99.9 % / Redundancy: 37.4 % / Rmerge(I) obs: 2.364 / Num. measured all: 104905 / Num. unique obs: 2806 / CC1/2: 0.92 / Rpim(I) all: 0.389 / Rrim(I) all: 2.396 / Χ2: 0.97 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4918: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FWM

2fwm


Resolution: 1.9→75.33 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 1927 4.96 %
Rwork0.1803 --
obs0.1827 38831 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→75.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 88 107 3816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093828
X-RAY DIFFRACTIONf_angle_d0.9295212
X-RAY DIFFRACTIONf_dihedral_angle_d13.721324
X-RAY DIFFRACTIONf_chiral_restr0.055600
X-RAY DIFFRACTIONf_plane_restr0.01681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.36591220.29792592X-RAY DIFFRACTION100
1.95-20.34291660.26072550X-RAY DIFFRACTION100
2-2.060.29331200.25282594X-RAY DIFFRACTION100
2.06-2.130.25521170.22852621X-RAY DIFFRACTION100
2.13-2.20.26141260.19382592X-RAY DIFFRACTION100
2.2-2.290.27291450.19032594X-RAY DIFFRACTION100
2.29-2.390.21791320.18522614X-RAY DIFFRACTION100
2.39-2.520.25641360.18282618X-RAY DIFFRACTION100
2.52-2.680.24391510.19722616X-RAY DIFFRACTION100
2.68-2.880.2461350.19282629X-RAY DIFFRACTION100
2.89-3.170.25971490.19482644X-RAY DIFFRACTION100
3.18-3.630.26061330.19012677X-RAY DIFFRACTION100
3.63-4.580.17631400.14682712X-RAY DIFFRACTION100
4.58-75.330.19031550.15962851X-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)
10.23430.2632-0.2811.02160.21450.72310.0363-0.05550.18250.1082-0.04630.2588-0.0046-0.074600.3988-0.00490.00050.4201-0.03990.433-13.113557.801614.2723
20.41780.194-0.24050.48670.11960.26550.0285-0.03440.03390.1577-0.0192-0.1391-0.07470.151300.4539-0.0138-0.06190.4217-0.00790.46183.492355.614310.622
30.11350.2066-0.04540.3588-0.06730.2797-0.0107-0.1172-0.20180.2258-0.01450.21150.0765-0.1837-0.00010.5261-0.01990.04360.45950.04790.3668-13.76418.161417.0116
40.26220.07580.04120.68930.2260.07830.0273-0.01060.05560.1059-0.02390.13550.0446-0.055500.4291-0.0170.00490.42420.02070.3936-10.742533.576714.1386
50.03460.0373-0.00090.27420.15370.13690.0864-0.0937-0.2146-0.04850.03670.61420.0445-0.4821-0.00040.42160.0071-0.06480.5925-0.02090.7717-17.135831.5486-1.7912
60.08260.0260.00050.19790.16810.1406-0.00130.03880.2529-0.1051-0.10310.2950.1205-0.0361-0.00010.4275-0.0065-0.04290.4118-0.01870.472-6.380727.6463-1.1608
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 72 )
4X-RAY DIFFRACTION4chain 'B' and (resid 73 through 168 )
5X-RAY DIFFRACTION5chain 'B' and (resid 169 through 205 )
6X-RAY DIFFRACTION6chain 'B' and (resid 206 through 251 )

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