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- PDB-6ovi: Crystal Structure of KDPG Aldolase from Legionella Pneumophila wi... -

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Basic information

Entry
Database: PDB / ID: 6ovi
TitleCrystal Structure of KDPG Aldolase from Legionella Pneumophila with pyruvate captured at low pH as a covalent carbinolamine intermediate
ComponentsKeto-deoxy-phosphogluconate aldolase
KeywordsLYASE / SSGCID / KDPG ALDOLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity
Similarity search - Function
KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2,2-bis(oxidanyl)propanoic acid / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of KDPG Aldolase from Legionella Pneumophila with pyruvate captured at low pH as a covalent carbinolamine intermediate
Authors: Davies, D.R. / Dranow, D.M.
History
DepositionMay 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Keto-deoxy-phosphogluconate aldolase
B: Keto-deoxy-phosphogluconate aldolase
C: Keto-deoxy-phosphogluconate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,45816
Polymers73,3153
Non-polymers1,14313
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-124 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.420, 79.140, 70.060
Angle α, β, γ (deg.)90.00, 117.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Keto-deoxy-phosphogluconate aldolase


Mass: 24438.301 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_01390 / Variant: ATCC 33152 / Plasmid: LEPNA.01267.A.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2S6FBD8, UniProt: Q5ZYF2*PLUS, 2-dehydro-3-deoxy-phosphogluconate aldolase, 4-hydroxy-2-oxoglutarate aldolase
#2: Chemical ChemComp-PVO / 2,2-bis(oxidanyl)propanoic acid


Type: L-peptide linking / Mass: 106.077 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: JCSG+ B1 (100 MM CITRATE, PH 4.0, 800 MM AMMONIUM SULFATE), 25% EG CRYO, TRAY 305567B1 PUCK LYZ8-4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2019
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 88619 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.37 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.66
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 27310 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUA

1eua


Resolution: 1.6→36.23 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 5084 6 %
Rwork0.157 --
obs0.159 84678 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.94 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 64 524 5167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064926
X-RAY DIFFRACTIONf_angle_d0.8136777
X-RAY DIFFRACTIONf_dihedral_angle_d12.6662954
X-RAY DIFFRACTIONf_chiral_restr0.056804
X-RAY DIFFRACTIONf_plane_restr0.005868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.26291610.26582280X-RAY DIFFRACTION83
1.6182-1.63720.23851500.25822353X-RAY DIFFRACTION86
1.6372-1.65720.28551450.2552363X-RAY DIFFRACTION86
1.6572-1.67820.31491610.25152496X-RAY DIFFRACTION89
1.6782-1.70020.30011370.24842476X-RAY DIFFRACTION89
1.7002-1.72350.22931680.21442470X-RAY DIFFRACTION89
1.7235-1.74820.26891620.22272531X-RAY DIFFRACTION92
1.7482-1.77430.26411480.21152541X-RAY DIFFRACTION92
1.7743-1.8020.23351530.19852568X-RAY DIFFRACTION92
1.802-1.83150.23871800.18742626X-RAY DIFFRACTION94
1.8315-1.86310.2321520.18762614X-RAY DIFFRACTION95
1.8631-1.8970.24021810.18452639X-RAY DIFFRACTION96
1.897-1.93350.21951630.1842687X-RAY DIFFRACTION96
1.9335-1.97290.18081520.17432690X-RAY DIFFRACTION97
1.9729-2.01580.21151730.17252745X-RAY DIFFRACTION98
2.0158-2.06270.20091780.17342744X-RAY DIFFRACTION98
2.0627-2.11430.18651600.16242724X-RAY DIFFRACTION98
2.1143-2.17140.18721820.16412728X-RAY DIFFRACTION99
2.1714-2.23530.18321930.15762740X-RAY DIFFRACTION99
2.2353-2.30750.2011890.16592725X-RAY DIFFRACTION99
2.3075-2.38990.18331920.16022772X-RAY DIFFRACTION99
2.3899-2.48560.18181790.16042749X-RAY DIFFRACTION99
2.4856-2.59870.19311680.16382771X-RAY DIFFRACTION99
2.5987-2.73570.22071940.1662729X-RAY DIFFRACTION100
2.7357-2.9070.17251570.15842829X-RAY DIFFRACTION100
2.907-3.13130.17231890.16042763X-RAY DIFFRACTION100
3.1313-3.44620.17741840.14692792X-RAY DIFFRACTION100
3.4462-3.94440.15381730.13672796X-RAY DIFFRACTION100
3.9444-4.96750.1251790.11672823X-RAY DIFFRACTION100
4.9675-36.23960.16111810.14952830X-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)
17.56842.4222-3.31793.7857-1.00476.5922-0.0162-0.0013-0.5048-0.16180.3308-0.28110.352-0.3899-0.28490.1568-0.0167-0.08440.3090.04080.194-43.5332-5.36232.4795
24.4279-1.37351.84463.3199-2.51326.96130.0518-0.5065-0.11830.10680.08810.2956-0.2113-0.3895-0.12330.1951-0.0082-0.0270.32870.05350.2169-53.2798-2.52086.7939
34.11570.6132.17196.96440.22837.24830.1237-0.212-0.5676-0.28460.15460.41510.3116-0.3923-0.19510.2381-0.0535-0.05450.39420.1160.3358-53.4122-10.67195.7866
45.5470.26830.6710.9114-0.72631.90670.0042-0.0233-0.4618-0.12750.03270.00690.1953-0.1512-0.02580.195-0.0178-0.01940.19380.020.2136-32.1238-8.26556.9817
58.6384-5.9367-3.78074.15463.00398.72030.08280.49020.8054-0.4281-0.0193-0.3606-0.4284-0.2715-0.18080.271-0.0232-0.04160.29830.07890.3804-34.86478.61530.4009
68.3085-1.7273-1.53573.3766-0.22930.9216-0.1222-0.06470.2933-0.03470.13330.1349-0.0567-0.05840.03290.2825-0.0097-0.03870.34270.02760.2797-49.3346.56972.3485
73.5834-0.73820.76261.4791-0.23613.94520.0052-0.0062-0.17720.00670.0362-0.02830.12970.0101-0.04510.210.01480.00840.1390.01470.2011-16.37342.014742.4912
80.76460.35870.561.24880.79992.3665-0.0028-0.01360.03330.0184-0.00060.0358-0.0147-0.14880.01430.17540.0280.03020.18180.02260.2007-23.46181.715730.9373
93.16281.193-1.52841.7603-0.31732.0921-0.20530.1964-0.0061-0.14480.07550.00880.26020.09280.15550.20060.00890.00440.21520.02730.1917-3.3886-5.5971-2.4822
101.84050.7637-1.04261.5818-0.50852.20050.06910.03840.2157-0.01610.00810.1003-0.09360.0969-0.13160.13310.0075-0.01520.1530.0110.1765-8.26072.63617.8783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 171 )
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 187 )
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 223 )
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 82 )
8X-RAY DIFFRACTION8chain 'B' and (resid 83 through 219 )
9X-RAY DIFFRACTION9chain 'C' and (resid 11 through 107 )
10X-RAY DIFFRACTION10chain 'C' and (resid 108 through 219 )

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