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- PDB-8q5a: Crystal structure of metal-dependent class II sulfofructosephosph... -

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Basic information

Entry
Database: PDB / ID: 8q5a
TitleCrystal structure of metal-dependent class II sulfofructosephosphate aldolase from Hafnia paralvei HpSqiA-Zn in complex with dihydroxyacetone phosphate (DHAP)
ComponentsKetose-bisphosphate aldolase
KeywordsLYASE / metal-dependent / aldolase / sulfoquinovose / sulfofructose phosphate
Function / homology
Function and homology information


aldehyde-lyase activity / carbohydrate metabolic process / zinc ion binding
Similarity search - Function
: / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase-type TIM barrel
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / Ketose-bisphosphate aldolase
Similarity search - Component
Biological speciesHafnia paralvei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003805/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Defining the molecular architecture, metal dependence, and distribution of metal-dependent class II sulfofructose-1-phosphate aldolases.
Authors: Sharma, M. / Kaur, A. / Madiedo Soler, N. / Lingford, J.P. / Epa, R. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionAug 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8894
Polymers33,5881
Non-polymers3013
Water1086
1
A: Ketose-bisphosphate aldolase
hetero molecules

A: Ketose-bisphosphate aldolase
hetero molecules

A: Ketose-bisphosphate aldolase
hetero molecules

A: Ketose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,55616
Polymers134,3534
Non-polymers1,20412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area9060 Å2
ΔGint-396 kcal/mol
Surface area38340 Å2
Unit cell
Length a, b, c (Å)64.605, 87.669, 103.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein Ketose-bisphosphate aldolase


Mass: 33588.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hafnia paralvei (bacteria) / Gene: kbaY / Plasmid: pET28a (+) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2A2MA06
#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-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: A crystal of the DHAP complex grew from 14 mg mL-1 enzyme in 50 mM Tris buffer pH 7.4 in a drop with 0.15 uL protein to 0.15 uL mother liquor soaked with SFP for 2 min, with the reservoir ...Details: A crystal of the DHAP complex grew from 14 mg mL-1 enzyme in 50 mM Tris buffer pH 7.4 in a drop with 0.15 uL protein to 0.15 uL mother liquor soaked with SFP for 2 min, with the reservoir solution containing 25% PEG 1,500 w/v, 0.1 M SPG (succinic acid, propionate, glycine) buffer pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→34.22 Å / Num. obs: 7522 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Χ2: 0.99 / Net I/σ(I): 17.7 / Num. measured all: 95222
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.439 / Num. measured all: 14614 / Num. unique obs: 1087 / CC1/2: 0.971 / Rpim(I) all: 0.123 / Rrim(I) all: 0.456 / Χ2: 0.95 / Net I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→34 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.866 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27408 382 5.1 %RANDOM
Rwork0.20793 ---
obs0.21133 7129 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.956 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å2-0 Å2-0 Å2
2--2.32 Å2-0 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 2.8→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 12 6 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122005
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161801
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.6462730
X-RAY DIFFRACTIONr_angle_other_deg0.4471.5764108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.95259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.75710276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5475.4681110
X-RAY DIFFRACTIONr_mcbond_other4.5475.4671110
X-RAY DIFFRACTIONr_mcangle_it7.0189.8161386
X-RAY DIFFRACTIONr_mcangle_other7.0199.8161387
X-RAY DIFFRACTIONr_scbond_it4.2095.361895
X-RAY DIFFRACTIONr_scbond_other4.1995.362892
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4139.881341
X-RAY DIFFRACTIONr_long_range_B_refined9.02347.72166
X-RAY DIFFRACTIONr_long_range_B_other9.02147.72167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 36 -
Rwork0.233 512 -
obs--99.46 %

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