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- PDB-6g3z: Sulfolobus sulfataricus 2-keto-3-deoxygluconate (KDG) aldolase co... -

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Basic information

Entry
Database: PDB / ID: 6g3z
TitleSulfolobus sulfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDPG
Components2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
KeywordsLYASE / 2-keto-3-deoxygluconate aldolase / Sulfolobus sulfataricus / 2-Dehydro-3-deoxy-6-phospho-D-gluconate
Function / homology
Function and homology information


2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity
Similarity search - Function
: / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-keto 3 deoxy 6 phospho gluconate / ISOPROPYL ALCOHOL / 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCrennell, S.J.
CitationJournal: Biochemistry / Year: 2018
Title: Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3- ...Title: Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate.
Authors: Zaitsev, V. / Johnsen, U. / Reher, M. / Ortjohann, M. / Taylor, G.L. / Danson, M.J. / Schonheit, P. / Crennell, S.J.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
B: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,24211
Polymers66,3052
Non-polymers9379
Water1,40578
1
A: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
B: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
hetero molecules

A: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
B: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,48322
Polymers132,6094
Non-polymers1,87418
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area13430 Å2
ΔGint-38 kcal/mol
Surface area41580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.865, 106.865, 245.636
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase


Mass: 33152.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: O54288, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
#2: Chemical ChemComp-ELE / 2-keto 3 deoxy 6 phospho gluconate


Mass: 258.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O9P
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 11% PEG 4000, 8% isopropanol, 0.1M HEPES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→92.548 Å / Num. obs: 35510 / % possible obs: 100 % / Redundancy: 75.8 % / Biso Wilson estimate: 60.22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.023 / Rrim(I) all: 0.146 / Net I/σ(I): 22.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 79.1 % / Rmerge(I) obs: 2.51 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3406 / CC1/2: 0.979 / Rpim(I) all: 0.392 / Rrim(I) all: 2.541 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W37

1w37


Resolution: 2.35→52.212 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 1686 4.8 %
Rwork0.1868 --
obs0.1892 35153 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→52.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 58 78 4788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094848
X-RAY DIFFRACTIONf_angle_d1.0036563
X-RAY DIFFRACTIONf_dihedral_angle_d14.7292962
X-RAY DIFFRACTIONf_chiral_restr0.052750
X-RAY DIFFRACTIONf_plane_restr0.006825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.41920.50331520.35552675X-RAY DIFFRACTION98
2.4192-2.49720.37371470.3082713X-RAY DIFFRACTION99
2.4972-2.58650.3411280.26612701X-RAY DIFFRACTION98
2.5865-2.690.35721270.23542736X-RAY DIFFRACTION99
2.69-2.81250.2681400.22612757X-RAY DIFFRACTION99
2.8125-2.96070.30491560.22812718X-RAY DIFFRACTION99
2.9607-3.14620.28181280.21342779X-RAY DIFFRACTION99
3.1462-3.38910.27211330.21212771X-RAY DIFFRACTION100
3.3891-3.73010.25391370.18982814X-RAY DIFFRACTION100
3.7301-4.26960.21561410.15662846X-RAY DIFFRACTION100
4.2696-5.37840.14791540.14262875X-RAY DIFFRACTION100
5.3784-52.22440.24241430.183082X-RAY DIFFRACTION100

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