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- PDB-5xsf: Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldola... -

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Basic information

Entry
Database: PDB / ID: 5xsf
TitleCrystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4 with 3-phosphoglycerate
ComponentsKHG/KDPG aldolase
KeywordsLYASE
Function / homology
Function and homology information


(4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase activity / metabolic process / cytoplasm
Similarity search - Function
KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / 3-HYDROXYPYRUVIC ACID / PHOSPHATE ION / KHG/KDPG aldolase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.962 Å
AuthorsSeo, P.W. / Kim, J.S.
CitationJournal: To Be Published
Title: Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4
Authors: Seo, P.W. / Kim, J.S.
History
DepositionJun 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: KHG/KDPG aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0775
Polymers21,5971
Non-polymers4804
Water2,702150
1
A: KHG/KDPG aldolase
hetero molecules

A: KHG/KDPG aldolase
hetero molecules

A: KHG/KDPG aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,23215
Polymers64,7923
Non-polymers1,44012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation80_555-z,x,-y1
Buried area7210 Å2
ΔGint-56 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.299, 186.299, 186.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21A-494-

HOH

31A-532-

HOH

41A-535-

HOH

51A-547-

HOH

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Components

#1: Protein KHG/KDPG aldolase


Mass: 21597.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: eda, kdgA, ZMO0997 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00384, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3PY / 3-HYDROXYPYRUVIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.6M Ammonium Sulfate, 0.1M CAPS (pH 10.5), 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.962→35.853 Å / Num. obs: 20372 / % possible obs: 99.5 % / Redundancy: 13.2 % / Net I/σ(I): 17.8
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 18.3 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.399 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xse

5xse


Resolution: 1.962→35.853 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 18.58
RfactorNum. reflection% reflection
Rfree0.2121 815 4 %
Rwork0.1907 --
obs0.1916 20372 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.962→35.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1511 0 28 150 1689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041585
X-RAY DIFFRACTIONf_angle_d0.6582160
X-RAY DIFFRACTIONf_dihedral_angle_d12.567968
X-RAY DIFFRACTIONf_chiral_restr0.05258
X-RAY DIFFRACTIONf_plane_restr0.005280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9625-2.08540.27281320.24663167X-RAY DIFFRACTION100
2.0854-2.24640.24221330.21933198X-RAY DIFFRACTION100
2.2464-2.47240.22341330.19843199X-RAY DIFFRACTION100
2.4724-2.830.19431350.20083230X-RAY DIFFRACTION100
2.83-3.5650.25021370.18813294X-RAY DIFFRACTION100
3.565-35.85920.181450.17093469X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.9983 Å / Origin y: 25.1353 Å / Origin z: -34.2592 Å
111213212223313233
T0.2525 Å20.0253 Å2-0.1242 Å2-0.1222 Å2-0.0514 Å2--0.3197 Å2
L1.3496 °2-0.0459 °20.6798 °2-0.8253 °2-0.2678 °2--1.3252 °2
S-0.0332 Å °-0.104 Å °0.2013 Å °-0.2026 Å °-0.0159 Å °0.1768 Å °-0.0425 Å °0.0557 Å °-0.036 Å °
Refinement TLS groupSelection details: all

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