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- PDB-7rgn: Crystal structure of putative fructose-1,6-bisphosphate aldolase ... -

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Basic information

Entry
Database: PDB / ID: 7rgn
TitleCrystal structure of putative fructose-1,6-bisphosphate aldolase from Candida auris
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / aldolase / zinc / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Disease
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase-type TIM barrel
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesCandida auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStogios, P.J. / Evdokimova, E. / Tan, K. / Di Leo, R. / 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 putative fructose-1,6-bisphosphate aldolase from Candida auris
Authors: Stogios, P.J.
History
DepositionJul 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6314
Polymers39,4131
Non-polymers2183
Water2,360131
1
A: Fructose-bisphosphate aldolase
hetero molecules

A: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2628
Polymers78,8272
Non-polymers4356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area5660 Å2
ΔGint-27 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.477, 64.477, 320.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

21A-608-

HOH

31A-629-

HOH

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Components

#1: Protein Fructose-bisphosphate aldolase / FBP aldolase


Mass: 39413.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida auris (fungus) / Gene: CAJCM15448_14580, CJI96_0004025, QG37_01471 / Plasmid: pMCSG53 / Details (production host): PIS48545.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
References: UniProt: A0A5C1DZF7, fructose-bisphosphate aldolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% isopropanol, 0.1 M bicine, pH 8.5, 30% w/v PEG1500, 1 mM zinc chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 21289 / % possible obs: 99.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 44.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.033 / Net I/σ(I): 21.72
Reflection shellResolution: 2.2→2.4 Å / Rmerge(I) obs: 1.44 / Num. unique obs: 1032 / CC1/2: 0.563 / Rpim(I) all: 0.493 / Χ2: 1.17 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6LNK

6lnk


Resolution: 2.2→29.91 Å / SU ML: 0.264 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.7991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 1923 9.39 %RANDOM
Rwork0.1942 18549 --
obs0.1983 20472 96.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 11 131 2780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252702
X-RAY DIFFRACTIONf_angle_d0.57583651
X-RAY DIFFRACTIONf_chiral_restr0.0408399
X-RAY DIFFRACTIONf_plane_restr0.0041473
X-RAY DIFFRACTIONf_dihedral_angle_d16.1991989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.35181210.31461127X-RAY DIFFRACTION85.42
2.25-2.310.34041250.29121193X-RAY DIFFRACTION88.58
2.32-2.380.32121270.24431233X-RAY DIFFRACTION92.2
2.38-2.460.26281260.24891253X-RAY DIFFRACTION93.87
2.46-2.550.33521330.24611289X-RAY DIFFRACTION95.44
2.55-2.650.27641330.23521294X-RAY DIFFRACTION97.14
2.65-2.770.30621390.24171326X-RAY DIFFRACTION98.19
2.77-2.920.30771410.21891351X-RAY DIFFRACTION98.68
2.92-3.10.2491410.2181351X-RAY DIFFRACTION98.61
3.1-3.340.28831400.22041355X-RAY DIFFRACTION99.47
3.34-3.670.21471410.19141379X-RAY DIFFRACTION99.48
3.67-4.20.18581460.15541403X-RAY DIFFRACTION99.87
4.2-5.290.19751500.15681444X-RAY DIFFRACTION99.56
5.29-29.910.22061600.17671551X-RAY DIFFRACTION98.67
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)
14.5509737854-4.052332128123.074238510768.26958758996-3.905815152776.460670658840.2375862098790.0606709065364-0.83292388486-0.5961145136980.07251532099930.4804092725471.14267884171-0.31009050455-0.4395026810580.495599776069-0.0485294459786-0.03607877879090.4628970308770.1362456202310.52768260364226.151185374325.9463640281139.047051465
21.89677143543-0.7696083632170.6151245836063.0617496381-1.79881115183.70720135953-0.0841009175405-0.293464092958-0.01471809878590.1183809697090.0447611565683-0.0396357882813-0.263371986712-0.1954925229540.03529690262510.2795788196370.00328656068846-0.04116610709960.4138262241570.1277254364310.35627512820422.935120842742.5376065237145.573709693
36.58096022081-1.35746703725-0.2216047529253.84514186152-1.476981437273.67826511924-0.0259702835351-0.738176156774-0.1118668081970.355367945202-0.0769689071267-0.529779816918-0.04315812964080.4946253211550.08108818793060.3186367408030.0100062926377-0.04133675726290.6796841264620.2633940959850.5422993498734.423573304629.9580741247156.556511571
42.130206331040.601357875091-0.5203237265588.78947844557-3.182751103724.48683686979-0.1438749230290.3853884655230.849390677022-0.791607978156-0.533553163557-0.958238714993-0.5027017334880.9589740687260.5812479915750.599754867709-0.135605450431-0.06840456015990.9570853598890.4280793954491.0524964668541.534511804753.8964332543129.370077392
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 26 )1 - 261 - 26
22chain 'A' and (resid 27 through 165 )27 - 16527 - 165
33chain 'A' and (resid 166 through 287 )166 - 287166 - 270
44chain 'A' and (resid 288 through 357 )288 - 357271 - 340

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