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

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Basic information

Entry
Database: PDB / ID: 8dqc
TitleCrystal structure of 3-dehydroquinate dehydratase I from Klebsiella oxytoca (I222 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
ACETATE ION / Riboflavin biosynthesis protein RibD
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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 (I222 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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
B: 3-dehydroquinate dehydratase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7616
Polymers82,5122
Non-polymers2494
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-104 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.800, 90.095, 222.401
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 8 through 10 and (name N...
21(chain B and ((resid 8 through 10 and (name N...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLN(chain A and ((resid 8 through 10 and (name N...AA8 - 108 - 10
12ALAALA(chain A and ((resid 8 through 10 and (name N...AA7 - 3757 - 375
13ALAALA(chain A and ((resid 8 through 10 and (name N...AA7 - 3757 - 375
14ALAALA(chain A and ((resid 8 through 10 and (name N...AA7 - 3757 - 375
15ALAALA(chain A and ((resid 8 through 10 and (name N...AA7 - 3757 - 375
21GLNGLN(chain B and ((resid 8 through 10 and (name N...BB8 - 108 - 10
22ALAALA(chain B and ((resid 8 through 10 and (name N...BB8 - 3758 - 375
23ALAALA(chain B and ((resid 8 through 10 and (name N...BB8 - 3758 - 375
24ALAALA(chain B and ((resid 8 through 10 and (name N...BB8 - 3758 - 375
25ALAALA(chain B and ((resid 8 through 10 and (name N...BB8 - 3758 - 375

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Components

#1: Protein 3-dehydroquinate dehydratase I


Mass: 41256.199 Da / Num. of mol.: 2 / 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 'Morpheus

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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: 2.7→70.9 Å / Num. obs: 20293 / % possible obs: 96 % / Redundancy: 7 % / Biso Wilson estimate: 68.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.025 / Rrim(I) all: 0.066 / Net I/σ(I): 18.3 / Num. measured all: 141641 / Scaling rejects: 3
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
2.7-2.777.20.6621120515480.9350.2630.7132.799.8
12.07-70.95.60.02915362750.9990.0130.03141.698

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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: 2.7→57.55 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 968 4.79 %
Rwork0.2214 19248 -
obs0.2232 20216 95.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.77 Å2 / Biso mean: 83.6019 Å2 / Biso min: 46.11 Å2
Refinement stepCycle: final / Resolution: 2.7→57.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5387 0 10 0 5397
Biso mean--89.78 --
Num. residues----726
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3165X-RAY DIFFRACTION8.546TORSIONAL
12B3165X-RAY DIFFRACTION8.546TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.840.36711360.33642817295399
2.84-3.020.32351590.27722792295199
3.02-3.250.29061370.282928522989100
3.25-3.580.32271010.2492233233478
3.58-4.10.26741530.21422672282594
4.1-5.160.20631460.188928863032100
5.16-57.550.24491360.20272996313299
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)
13.78390.0543-0.58351.87542.20344.81580.22390.0184-0.3443-0.2012-0.18610.03711.1179-0.1454-0.02891.4238-0.0313-0.12930.4956-0.00270.674351.71643.289818.7205
20.83860.31611.20691.84691.95324.74750.11620.3014-0.9048-0.75740.6589-0.47871.12191.0569-0.95351.57530.1727-0.11310.7582-0.17250.903362.9796-2.97320.4852
32.2966-0.06571.67580.1614-0.05893.15940.16570.3525-0.2358-1.0359-0.1149-0.18370.7831.29770.0991.12010.0224-0.05090.58-0.05620.905162.75889.249324.9599
41.46271.07810.08243.3277-2.29092.35850.12030.07610.174-0.2660.19310.268-0.2532-0.3637-0.28440.6063-0.03-0.00340.6277-0.00260.603848.094528.623940.7356
55.1457-0.26911.84623.70551.87937.675-0.13340.81570.1944-0.3755-0.17650.91430.7161-1.040.37770.5849-0.2046-0.11180.77210.06840.705440.630117.009437.5185
65.6143-0.1634-1.55533.076-0.6899.5774-0.2358-0.6398-0.16660.33350.09470.01650.5661-0.37970.19820.6305-0.0762-0.09330.41360.0570.482952.044515.420452.6987
72.5851-2.35231.3355.4803-2.12045.2451-0.042-0.01310.38050.0982-0.1284-0.3627-0.20870.17840.19350.4223-0.10040.00670.50610.02160.606957.807833.198537.8841
80.6468-0.7647-0.00531.7273-0.75153.98620.26950.1354-0.2319-1.3045-0.17980.25360.40480.115-0.07071.2851-0.0127-0.22740.50790.01030.689252.477862.1832.7335
92.10391.456-0.73858.31230.48510.3901-0.0115-0.1206-0.32240.21610.0785-0.9392-0.03540.1962-0.0170.5864-0.01-0.05220.66270.0820.586565.45151.560432.1212
104.5267-2.9676-1.37763.06222.48892.6906-0.0546-0.4340.15290.01260.2148-0.3957-0.29161.1695-0.15060.6853-0.10030.06590.68530.11940.616469.599663.359527.0799
111.27760.9488-0.26555.64060.27982.9882-0.0812-0.11870.31260.39580.11680.2059-0.6157-0.1198-0.0170.54440.0110.00550.45230.03390.530756.412466.016132.9714
122.4355-1.0736-1.27236.9528-0.34634.30290.0331-0.11920.14780.1932-0.09760.5178-0.4259-0.30750.04810.5141-0.0546-0.05780.526-0.07680.642753.307545.023734.0092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 91 )A7 - 91
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 125 )A92 - 125
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 152 )A126 - 152
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 208 )A153 - 208
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 241 )A209 - 241
6X-RAY DIFFRACTION6chain 'A' and (resid 242 through 309 )A242 - 309
7X-RAY DIFFRACTION7chain 'A' and (resid 310 through 375 )A310 - 375
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 163 )B8 - 163
9X-RAY DIFFRACTION9chain 'B' and (resid 164 through 208 )B164 - 208
10X-RAY DIFFRACTION10chain 'B' and (resid 209 through 263 )B209 - 263
11X-RAY DIFFRACTION11chain 'B' and (resid 264 through 329 )B264 - 329
12X-RAY DIFFRACTION12chain 'B' and (resid 330 through 375 )B330 - 375

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