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- PDB-8dq9: Crystal structure of GDP bound 3-dehydroquinate dehydratase I fro... -

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Entry
Database: PDB / ID: 8dq9
TitleCrystal structure of GDP bound 3-dehydroquinate dehydratase I from Klebsiella oxytoca
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
GUANOSINE-5'-DIPHOSPHATE / Riboflavin biosynthesis protein RibD
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 GDP bound 3-dehydroquinate dehydratase I from Klebsiella oxytoca
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)83,1577
Polymers82,5122
Non-polymers6455
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-87 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.342, 89.761, 223.744
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 10 through 174 or (resid 175...
21(chain B and (resid 10 through 40 or (resid 41...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLY(chain A and (resid 10 through 174 or (resid 175...AA10 - 17410 - 174
12GLUGLUGLNGLN(chain A and (resid 10 through 174 or (resid 175...AA175 - 177175 - 177
13GLNGLNALAALA(chain A and (resid 10 through 174 or (resid 175...AA10 - 37510 - 375
14GLNGLNALAALA(chain A and (resid 10 through 174 or (resid 175...AA10 - 37510 - 375
15GLNGLNALAALA(chain A and (resid 10 through 174 or (resid 175...AA10 - 37510 - 375
16GLNGLNALAALA(chain A and (resid 10 through 174 or (resid 175...AA10 - 37510 - 375
21GLNGLNVALVAL(chain B and (resid 10 through 40 or (resid 41...BB10 - 4010 - 40
22LYSLYSLYSLYS(chain B and (resid 10 through 40 or (resid 41...BB4141
23GLNGLNALAALA(chain B and (resid 10 through 40 or (resid 41...BB10 - 37510 - 375
24GLNGLNALAALA(chain B and (resid 10 through 40 or (resid 41...BB10 - 37510 - 375
25GLNGLNALAALA(chain B and (resid 10 through 40 or (resid 41...BB10 - 37510 - 375
26GLNGLNALAALA(chain B and (resid 10 through 40 or (resid 41...BB10 - 37510 - 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-CL / CHLORIDE ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus H8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM ...Details: Morpheus H8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine, KloxA.17380.a.B1.PW39095 at 5 mg/mL with 2.5 GDP added. Tray: plate 12679, well H8 drop 3, Puck: PSL1316, 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: 2.8→83.31 Å / Num. obs: 18874 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 68.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.045 / Rrim(I) all: 0.12 / Net I/σ(I): 11.5 / Num. measured all: 133275 / Scaling rejects: 27
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
2.8-2.877.10.978974013630.8790.3911.0552.2100
12.52-83.315.30.05812832400.9950.0280.06525.196.8

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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: 2.8→55.94 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2791 931 4.94 %
Rwork0.2304 17907 -
obs0.2329 18838 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.09 Å2 / Biso mean: 76.5613 Å2 / Biso min: 45.41 Å2
Refinement stepCycle: final / Resolution: 2.8→55.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 32 10 5493
Biso mean--87.97 61.34 -
Num. residues----715
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3072X-RAY DIFFRACTION13.201TORSIONAL
12B3072X-RAY DIFFRACTION13.201TORSIONAL
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 (%)
2.8-2.950.3651080.344625252633100
2.95-3.130.35131270.317425172644100
3.13-3.370.32431380.266425262664100
3.37-3.710.31481210.252825692690100
3.71-4.250.2591500.20825192669100
4.25-5.350.25141400.190825842724100
5.36-55.940.25931470.21822667281499
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)
12.33470.1381.17720.39380.94674.26440.34540.0056-0.2781-0.2941-0.2801-0.20621.3077-0.3992-0.00291.2582-0.042-0.05670.4390.01410.761912.90896.705919.8708
20.4393-0.5447-0.90673.06163.28084.5370.2169-0.1229-0.90820.16140.5017-0.36221.72331.0402-0.51951.8740.2593-0.24320.5246-0.04110.981722.0526-1.90718.7002
31.4089-0.84010.172.4714-2.27242.23570.2398-0.0241-0.0904-0.4830.0937-0.1640.0894-0.1457-0.35120.483-0.0718-0.0450.3299-0.01510.544113.687525.016538.2392
43.20560.37540.38622.69840.27594.67920.03180.01230.0169-0.0939-0.04990.19640.4006-0.4143-0.0030.4944-0.0855-0.05030.29430.03130.46219.521416.283148.4587
52.7166-1.0922-0.32065.6062-2.08765.43130.0796-0.05750.31150.1026-0.1225-0.2631-0.10590.310.02820.2919-0.07480.00990.29210.02280.534718.614130.791638.5205
62.032-0.7586-1.88072.53333.33125.6891-0.1112-0.0059-0.3411-1.443-0.3910.70331.01680.35210.31271.29810.0539-0.02750.40250.06530.823419.150256.88712.3033
73.3099-0.5954-0.57060.37891.06143.7278-0.2415-0.49620.2825-0.7177-0.42060.10780.29450.11170.35091.35160.13550.10740.36750.03340.71823.99864.2002-2.5337
83.8705-0.6413-1.25473.3161.12292.6880.2408-0.2492-0.1827-1.05640.0813-0.21550.3027-0.2044-0.26721.287-0.0526-0.2670.26760.03520.598311.547467.1845-0.8784
91.1195-2.03652.662.4037-2.68165.49270.1-0.1674-0.4877-0.76730.16030.41130.3753-0.246-0.28240.6519-0.1294-0.1250.44440.11210.769910.412361.590411.4167
101.04461.2283-0.94925.63590.36651.56060.2369-0.1842-0.43720.13480.159-0.16330.88690.2893-0.38380.61250.0201-0.09650.48920.04140.483928.467151.766432.4095
113.4488-2.5304-3.85283.35073.09178.1919-0.0904-0.2098-0.2615-0.2170.3351-0.1547-0.3241.4368-0.20720.40320.02370.03930.62130.02860.710432.823359.506921.3513
127.0301-0.7434-2.87585.86250.22825.75760.1208-0.52561.54010.82260.5509-0.6275-2.01071.0046-0.45560.7731-0.0377-0.0730.4722-0.01150.741831.570471.961236.6735
135.5628-0.11910.81519.0112.32516.842-1.0117-0.531-0.0631.57890.32981.094-0.1618-1.63460.240.9440.19420.09710.24430.13110.588316.299872.164234.8326
141.35330.0459-0.75997.0426-3.59095.10610.2876-0.13250.55520.1170.20360.5669-0.5882-0.1685-0.46310.35560.05180.03560.37850.01790.573618.647560.70931.4684
153.69040.5019-0.89194.42790.46043.0316-0.0548-0.1931-0.11160.40310.05950.62730.0289-0.2621-0.01560.356-0.03680.04350.25360.03720.554615.743546.791933.8752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 58 )A10 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 135 )A59 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 208 )A136 - 208
4X-RAY DIFFRACTION4chain 'A' and (resid 209 through 298 )A209 - 298
5X-RAY DIFFRACTION5chain 'A' and (resid 299 through 375 )A299 - 375
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 43 )B10 - 43
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 71 )B44 - 71
8X-RAY DIFFRACTION8chain 'B' and (resid 72 through 117 )B72 - 117
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 164 )B118 - 164
10X-RAY DIFFRACTION10chain 'B' and (resid 165 through 208 )B165 - 208
11X-RAY DIFFRACTION11chain 'B' and (resid 209 through 241 )B209 - 241
12X-RAY DIFFRACTION12chain 'B' and (resid 242 through 274 )B242 - 274
13X-RAY DIFFRACTION13chain 'B' and (resid 275 through 298 )B275 - 298
14X-RAY DIFFRACTION14chain 'B' and (resid 299 through 318 )B299 - 318
15X-RAY DIFFRACTION15chain 'B' and (resid 319 through 375 )B319 - 375

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