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

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Basic information

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


(R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / 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
2-dehydro-3-deoxy-phosphogluconate aldolase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsSeo, P.W. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Nation Research Foundation Korea, Republic Of
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 13, 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
B: KHG/KDPG aldolase
C: KHG/KDPG aldolase


Theoretical massNumber of molelcules
Total (without water)64,5793
Polymers64,5793
Non-polymers00
Water11,890660
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-22 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.695, 83.025, 117.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KHG/KDPG aldolase


Mass: 21526.324 Da / Num. of mol.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 25%(w/v) polyethylene glycol 8,000, 0.1M Bis-tris (pH 5.5)

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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 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 57557 / % possible obs: 98.5 % / Redundancy: 8.2 % / Rsym value: 0.077 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.43 / % possible all: 95.8

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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: 3onp

3onp


Resolution: 1.799→35.351 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 2879 5 %
Rwork0.19 --
obs0.1921 57557 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→35.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4502 0 0 660 5162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054595
X-RAY DIFFRACTIONf_angle_d0.7076252
X-RAY DIFFRACTIONf_dihedral_angle_d11.4172830
X-RAY DIFFRACTIONf_chiral_restr0.05759
X-RAY DIFFRACTIONf_plane_restr0.006808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7989-1.82840.37421300.34522465X-RAY DIFFRACTION95
1.8284-1.85990.34691310.31632498X-RAY DIFFRACTION96
1.8599-1.89370.34261320.28922502X-RAY DIFFRACTION96
1.8937-1.93020.29491350.27912565X-RAY DIFFRACTION97
1.9302-1.96960.29371340.25482540X-RAY DIFFRACTION98
1.9696-2.01240.27231340.24822537X-RAY DIFFRACTION98
2.0124-2.05920.28791350.23632574X-RAY DIFFRACTION98
2.0592-2.11070.28161350.22422575X-RAY DIFFRACTION99
2.1107-2.16770.22781360.20392568X-RAY DIFFRACTION98
2.1677-2.23150.2431370.19342605X-RAY DIFFRACTION99
2.2315-2.30350.22911370.19352613X-RAY DIFFRACTION99
2.3035-2.38580.25031370.18922596X-RAY DIFFRACTION99
2.3858-2.48130.22861380.18112608X-RAY DIFFRACTION99
2.4813-2.59420.22611360.18382616X-RAY DIFFRACTION99
2.5942-2.7310.24941400.18782637X-RAY DIFFRACTION99
2.731-2.9020.2151380.18992642X-RAY DIFFRACTION99
2.902-3.12590.23791390.18192620X-RAY DIFFRACTION100
3.1259-3.44030.20191410.17452685X-RAY DIFFRACTION100
3.4403-3.93750.20011410.15242689X-RAY DIFFRACTION100
3.9375-4.95870.16451430.13312715X-RAY DIFFRACTION100
4.9587-35.35770.18851500.15062828X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.2895 Å / Origin y: -3.6222 Å / Origin z: -9.6936 Å
111213212223313233
T0.1115 Å2-0.0049 Å2-0.0081 Å2-0.0653 Å20.0001 Å2--0.1277 Å2
L0.6699 °2-0.0105 °20.1473 °2-0.3688 °20.0898 °2--0.9627 °2
S-0.0075 Å °-0.0462 Å °0.0668 Å °-0.0147 Å °-0.0205 Å °-0.0346 Å °-0.0218 Å °-0.0174 Å °0.0204 Å °
Refinement TLS groupSelection details: all

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