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- PDB-8dqb: Crystal structure of 3-dehydroquinate dehydratase I from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 8dqb
TitleCrystal structure of 3-dehydroquinate dehydratase I from Klebsiella oxytoca (I23 Form)
Components3-dehydroquinate dehydratase I
KeywordsHYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


5-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase
Similarity search - Function
Riboflavin biosynthesis protein RibD / Riboflavin-specific deaminase, C-terminal / Bacterial bifunctional deaminase-reductase, C-terminal / RibD C-terminal domain / Cytidine and deoxycytidylate deaminase zinc-binding region / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Riboflavin biosynthesis protein RibD
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of 3-dehydroquinate dehydratase I from Klebsiella oxytoca (I23 Form)
Authors: Liu, L. / Seibold, S. / Battaile, K.P. / Lovell, S.
History
DepositionJul 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3873
Polymers41,2561
Non-polymers1312
Water55831
1
A: 3-dehydroquinate dehydratase I
hetero molecules

A: 3-dehydroquinate dehydratase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7746
Polymers82,5122
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3840 Å2
ΔGint-148 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.124, 164.124, 164.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein 3-dehydroquinate dehydratase I /


Mass: 41256.199 Da / Num. of mol.: 1 / Fragment: KloxA.17380.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Plasmid: KloxA.17380.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8F3UXX5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 4.46 Å3/Da / Density % sol: 72.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus A2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2,KloxA.17380.a.B1.PW39095 at 5 mg/mL with 2.5 GDP added, no electron ...Details: Morpheus A2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 30 mM MgCl2 and 30 mM CaCl2,KloxA.17380.a.B1.PW39095 at 5 mg/mL with 2.5 GDP added, no electron density observed for the GDP, Tray: plate 12679, well A2 drop 3, Puck: PSL1405, Cryo: DIRECT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 7, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→116.05 Å / Num. obs: 25537 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 56.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 18.6 / Num. measured all: 264742 / Scaling rejects: 42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.5710.71.1582024518860.7440.3691.2162.2100
11.18-116.058.70.02727693180.9990.010.02955.499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O7P

2o7p


Resolution: 2.5→41.03 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 1292 5.07 %
Rwork0.2032 24212 -
obs0.205 25504 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.86 Å2 / Biso mean: 58.4844 Å2 / Biso min: 34.46 Å2
Refinement stepCycle: final / Resolution: 2.5→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 2 31 2884
Biso mean--63.85 52.26 -
Num. residues----370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.60.39761560.292326522808100
2.6-2.720.28421480.255826612809100
2.72-2.860.30851470.259626552802100
2.86-3.040.3121260.251826822808100
3.04-3.280.30341230.271227152838100
3.28-3.610.32841420.213826582800100
3.61-4.130.20941620.19326942856100
4.13-5.20.18871350.165427202855100
5.2-41.030.18741530.16872775292899
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)
12.6398-0.7341-0.18981.53811.43423.83270.10890.01730.1506-0.1106-0.07390.19420.0104-0.2781-0.03840.6023-0.0893-0.04950.3470.00720.43866.6613-29.4802-11.1242
20.40540.60570.62733.76333.00033.016-0.0093-0.03140.00660.3011-0.01130.14650.2457-0.10450.04880.5375-0.02250.01360.37840.00620.377573.7481-20.31686.216
33.2305-0.08831.011.94521.35871.3125-0.1024-0.17220.3165-0.0555-0.15520.3511-0.132-0.56270.25350.47290.0004-0.03120.4672-0.08380.389960.513-11.834214.7002
47.2524-3.2029-2.38853.4688-1.02622.93710.0191-0.2182-0.16850.0966-0.09050.29440.364-0.5580.07230.7193-0.22780.01380.5777-0.05530.392562.0987-24.143625.893
51.08520.6917-0.33552.58680.11552.2014-0.0331-0.0692-0.1014-0.1076-0.08310.10840.1426-0.09450.11850.55460.0272-0.01250.349-0.02880.330578.5285-9.481917.6002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 117 )A3 - 117
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 181 )A118 - 181
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 250 )A182 - 250
4X-RAY DIFFRACTION4chain 'A' and (resid 251 through 298 )A251 - 298
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 375 )A299 - 375

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