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- PDB-6voq: Crystal structure of YgbL, a putative aldolase/epimerase/decarbox... -

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Basic information

Entry
Database: PDB / ID: 6voq
TitleCrystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Klebsiella pneumoniae
ComponentsAldolase
KeywordsLYASE / PUTATIVE LYASE / EPIMERASE / ALDOLASE / ISOMERASE / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES
Function / homology
Function and homology information


3-dehydro-4-phosphotetronate decarboxylase / L-fuculose-phosphate aldolase activity / pentose catabolic process / metal ion binding / cytosol
Similarity search - Function
: / : / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily
Similarity search - Domain/homology
3-oxo-tetronate 4-phosphate decarboxylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsStogios, P.J. / Evdokimova, E. / McChesney, C. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Klebsiella pneumoniae
Authors: Stogios, P.J.
History
DepositionJan 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8093
Polymers22,7081
Non-polymers1012
Water2,720151
1
A: Aldolase
hetero molecules

A: Aldolase
hetero molecules

A: Aldolase
hetero molecules

A: Aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,23512
Polymers90,8314
Non-polymers4038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area10160 Å2
ΔGint-223 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.436, 76.436, 181.682
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

21A-526-

HOH

31A-541-

HOH

41A-544-

HOH

51A-548-

HOH

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Components

#1: Protein Aldolase / FucA aldolase-like protein / L-fuculose phosphate aldolase / Ribulose-5-phosphate 4-epimerase


Mass: 22707.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: fucA_2, fucA_1, fucA_3, BL124_00025510, C3483_13535, C3F39_01215, C7V41_22435, CWN54_08000, DD581_15345, DM059_14180, EAO17_27025, EXT45_05660, FAM48_01070, FAQ72_03260, FAQ97_05405, FAS39_ ...Gene: fucA_2, fucA_1, fucA_3, BL124_00025510, C3483_13535, C3F39_01215, C7V41_22435, CWN54_08000, DD581_15345, DM059_14180, EAO17_27025, EXT45_05660, FAM48_01070, FAQ72_03260, FAQ97_05405, FAS39_03255, FNY87_25290, NCTC11679_02859, NCTC13465_01855, NCTC1936_02659, NCTC5047_00576, NCTC9140_04285, NCTC9601_02686, NCTC9645_06176, NCTC9661_03377, PMK1_03924, SAMEA24002668_05560, SAMEA4364603_02467, SK89_00182
Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic / References: UniProt: Q0QC76, L-fuculose-phosphate aldolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Na Tartrate, 0.1M TRIS pH 8.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→25 Å / Num. obs: 9859 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 35.89 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.037 / Net I/σ(I): 18.74
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 490 / CC1/2: 0.91 / Rpim(I) all: 0.233

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OPI

2opi


Resolution: 2.49→24.58 Å / SU ML: 0.2477 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.2302
RfactorNum. reflection% reflectionSelection details
Rfree0.211 493 5 %THROUGHOUT
Rwork0.1563 ---
obs0.159 9859 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.27 Å2
Refinement stepCycle: LAST / Resolution: 2.49→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 2 151 1748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621628
X-RAY DIFFRACTIONf_angle_d0.79122216
X-RAY DIFFRACTIONf_chiral_restr0.0498254
X-RAY DIFFRACTIONf_plane_restr0.006291
X-RAY DIFFRACTIONf_dihedral_angle_d3.1398979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.740.25031180.18982256X-RAY DIFFRACTION98.42
2.74-3.130.23141220.18772299X-RAY DIFFRACTION100
3.13-3.940.22031230.14742340X-RAY DIFFRACTION100
3.94-24.580.18341300.14082471X-RAY DIFFRACTION100
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)
12.81787180952-0.0685360398992-0.2981377482189.359412219795.351098253455.80730678189-0.0168010237083-0.5599246198830.03079414236220.946616387985-0.2168215691040.6030827765030.596957025799-0.3279736319490.2549491110580.384105733832-0.0660245762307-0.01416485665460.459395510495-0.03191714415920.2537599994281.4322818503517.865051090139.7885218096
25.143128081481.730070320381.262431570835.970967297022.023542192275.336403234840.0483624427385-0.453010865359-0.256116151325-0.07536354073630.15689337864-0.4647332945780.1240806940370.272097433537-0.1579106863390.354213826196-0.00108945022114-0.03727964281560.3534681094760.006109426423160.2400621412238.4244098478819.446288951735.5709886492
30.5619121423390.5288898967920.3203373528682.067435848340.4751639264973.304860286030.0138562742069-0.142482758490.1644288484920.2657964295750.0513922262661-0.0998517037537-0.287710448570.350639502094-0.0296551843250.282356642075-0.00920709067053-0.02018207931840.302478767554-0.04455151015020.3663610465978.3283338157924.914700185527.4030492357
46.31332112947-1.660973076022.019139961474.862941196621.899182027882.043313224280.115087466867-0.2219441463390.308167705185-0.025604632552-0.1125010566150.222616917296-0.130405534612-0.213209410261-0.02801601609890.318345207833-0.0240867925774-0.01562056049130.2315788069980.05159235632940.264960815952-4.5671820327620.760339872512.6737476925
52.98595793692-1.65061200882-2.568560132563.96422907962.135426377154.153256092960.156583212965-0.05659126711020.277841919191-0.2517051799180.040377229639-0.197868234652-0.2292323474570.173660945633-0.1919888308150.303372414592-0.0209454779252-0.05802736151240.214248669871-0.01254288226960.3037779099067.5611327073426.173006685818.4627762905
62.506333897612.265651197442.567874123038.623700366496.246238658624.97307933233-0.0654594653499-0.2039510773710.09177672074350.327881327357-0.3366680745460.483518868190.299753493584-0.3992383240530.4242165628080.2297842228220.0264939563725-0.0306964878570.26505175056-0.0159468749410.312176530727-4.3898030254513.677741554321.3734789105
77.99433877118-3.08617664787-1.413034001271.768743333330.7664715269535.409263021610.3582729995190.3627036384690.788188905118-0.704487788174-0.00160286475044-0.467437884906-0.702784215721-0.0289278250614-0.2397556780580.30530338192-0.06574956704970.03482409398930.3035025317080.02098646547250.31686675074-14.453306374417.32980939098.22813157777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 168 )
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 189 )
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 206 )

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