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- PDB-8q58: Crystal structure of metal-dependent classII sulfofructosephospha... -

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Basic information

Entry
Database: PDB / ID: 8q58
TitleCrystal structure of metal-dependent classII sulfofructosephosphate aldolase (SFPA) from Hafnia paralvei HpSqiA-Zn
ComponentsKetose-bisphosphate aldolase
KeywordsLYASE / metal-dependent / aldolase / sulfoquinovose / sulfofructose phosphate
Function / homology: / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / aldehyde-lyase activity / Aldolase-type TIM barrel / carbohydrate metabolic process / zinc ion binding / Ketose-bisphosphate aldolase
Function and homology information
Biological speciesHafnia paralvei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

Deposited unit
A: Ketose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7193
Polymers33,5881
Non-polymers1312
Water2,198122
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)134,87612
Polymers134,3534
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area7890 Å2
ΔGint-388 kcal/mol
Surface area36680 Å2
Unit cell
Length a, b, c (Å)60.332, 88.490, 126.805
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-426-

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 BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate dibasic monohydrate and 20% w/v PEG (polyethylene glycol) 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→63.4 Å / Num. obs: 37727 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.017 / Rrim(I) all: 0.064 / Χ2: 0.96 / Net I/σ(I): 20.2 / Num. measured all: 512681
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.81 / Num. measured all: 26484 / Num. unique obs: 1987 / CC1/2: 0.917 / Rpim(I) all: 0.229 / Rrim(I) all: 0.842 / Χ2: 0.97 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→63.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.942 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20052 1879 5 %RANDOM
Rwork0.18545 ---
obs0.18623 35843 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.329 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å20 Å2
2--0.31 Å20 Å2
3----1.99 Å2
Refinement stepCycle: 1 / Resolution: 1.7→63.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 2 122 2126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122077
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161994
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.6432815
X-RAY DIFFRACTIONr_angle_other_deg0.571.5754581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3975279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.132511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30610352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02457
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_it3.2043.2651083
X-RAY DIFFRACTIONr_mcbond_other3.2013.2651083
X-RAY DIFFRACTIONr_mcangle_it4.2755.8441352
X-RAY DIFFRACTIONr_mcangle_other4.2775.8471353
X-RAY DIFFRACTIONr_scbond_it4.1313.537994
X-RAY DIFFRACTIONr_scbond_other4.1293.539995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8946.3851457
X-RAY DIFFRACTIONr_long_range_B_refined6.73530.912318
X-RAY DIFFRACTIONr_long_range_B_other6.71230.752301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 129 -
Rwork0.254 2600 -
obs--99.93 %

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