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- PDB-8i05: Crystal structure of Escherichia coli glyoxylate carboligase doub... -

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Basic information

Entry
Database: PDB / ID: 8i05
TitleCrystal structure of Escherichia coli glyoxylate carboligase double mutant
ComponentsGlyoxylate carboligase
KeywordsLIGASE / GCL
Function / homology
Function and homology information


tartronate-semialdehyde synthase / tartronate-semialdehyde synthase activity / glycolate catabolic process / acetolactate synthase complex / glyoxylate catabolic process / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / FAD binding / flavin adenine dinucleotide binding ...tartronate-semialdehyde synthase / tartronate-semialdehyde synthase activity / glycolate catabolic process / acetolactate synthase complex / glyoxylate catabolic process / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / FAD binding / flavin adenine dinucleotide binding / magnesium ion binding / identical protein binding
Similarity search - Function
: / Glyoxylate carboligase / Thiamine pyrophosphate enzyme / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / THIAMINE DIPHOSPHATE / 2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE / Glyoxylate carboligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsKim, J.H. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose.
Authors: Kim, J.H. / Cheon, H. / Jo, H.J. / Kim, J.W. / Kim, G.Y. / Seo, H.R. / Seo, P.W. / Kim, J.S. / Park, J.B.
History
DepositionJan 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxylate carboligase
B: Glyoxylate carboligase
C: Glyoxylate carboligase
D: Glyoxylate carboligase
E: Glyoxylate carboligase
F: Glyoxylate carboligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,78040
Polymers389,0866
Non-polymers9,69434
Water40,4442245
1
A: Glyoxylate carboligase
B: Glyoxylate carboligase
hetero molecules

A: Glyoxylate carboligase
B: Glyoxylate carboligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,88628
Polymers259,3914
Non-polymers6,49524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area21610 Å2
ΔGint-129 kcal/mol
Surface area69450 Å2
MethodPISA
2
C: Glyoxylate carboligase
D: Glyoxylate carboligase
E: Glyoxylate carboligase
F: Glyoxylate carboligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,83726
Polymers259,3914
Non-polymers6,44722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21620 Å2
ΔGint-130 kcal/mol
Surface area69190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.172, 189.172, 246.506
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-704-

MG

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Glyoxylate carboligase / Tartronate-semialdehyde synthase


Mass: 64847.652 Da / Num. of mol.: 6 / Mutation: N283Q, R484M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: gcl, b0507, JW0495 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AEP7, tartronate-semialdehyde synthase

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Non-polymers , 5 types, 2279 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-UQ0 / 2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE


Mass: 182.173 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H10O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2245 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 mM Tris-HCl (pH 8.0), 0.5 M sodium chloride, 40 mM dithiothreitol, 0.5% (v/v) polyethylene glycol 6000 (PEG6K)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 253025 / % possible obs: 96.3 % / Redundancy: 10.1 % / Biso Wilson estimate: 30.87 Å2 / Rmerge(I) obs: 0.999 / Χ2: 0.06 / Net I/σ(I): 2.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.149.51.697229450.399191.1
2.14-2.189.51.53229110.399191.4
2.18-2.229.51.422230440.4191.4
2.22-2.269.31.177230830.416191.5
2.26-2.318.81.152231900.409191.9
2.31-2.379.31.041233050.397192.9
2.37-2.429.70.924237070.426194.1
2.42-2.499.60.818240330.434195.3
2.49-2.569.50.673242910.455196.4
2.56-2.659.40.583245740.478197.6
2.65-2.749.30.517248100.482198.4
2.74-2.858.80.419246090.508197.9
2.85-2.989.90.344251220.555199.7
2.98-3.1410.20.259251400.638199.9
3.14-3.3310.50.21251850.723199.9
3.33-3.5910.40.154251650.846199.9
3.59-3.9510.50.124249700.993199
3.95-4.5211.60.101251700.962199.9
4.52-5.712.10.091249150.941199
5.7-5013.70.067250870.896199.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
PHENIXv2.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→49.81 Å / SU ML: 0.2629 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.252
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 9966 3.95 %
Rwork0.2088 242271 -
obs0.2104 252237 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.38 Å2
Refinement stepCycle: LAST / Resolution: 2.09→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27239 0 640 2245 30124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828457
X-RAY DIFFRACTIONf_angle_d0.992338705
X-RAY DIFFRACTIONf_chiral_restr0.06114314
X-RAY DIFFRACTIONf_plane_restr0.01024992
X-RAY DIFFRACTIONf_dihedral_angle_d15.711510331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.120.38712870.34666960X-RAY DIFFRACTION84.62
2.12-2.140.35413140.34027596X-RAY DIFFRACTION91.58
2.14-2.170.38553110.31987560X-RAY DIFFRACTION91.73
2.17-2.190.35323130.31687612X-RAY DIFFRACTION91.92
2.19-2.220.36373120.31057598X-RAY DIFFRACTION91.86
2.22-2.250.3113160.2917665X-RAY DIFFRACTION92.48
2.25-2.290.32493180.29417727X-RAY DIFFRACTION93.17
2.29-2.320.33253180.28767722X-RAY DIFFRACTION93.11
2.32-2.360.34043200.27247799X-RAY DIFFRACTION94.37
2.36-2.390.30243250.26347908X-RAY DIFFRACTION95.28
2.39-2.440.30673270.25957994X-RAY DIFFRACTION96.45
2.44-2.480.29153320.24058057X-RAY DIFFRACTION97.15
2.48-2.530.24123360.23758165X-RAY DIFFRACTION97.96
2.53-2.580.27963360.23848166X-RAY DIFFRACTION98.52
2.58-2.640.30233380.23148218X-RAY DIFFRACTION98.96
2.64-2.70.29443400.23348258X-RAY DIFFRACTION99.31
2.7-2.760.29093400.23388279X-RAY DIFFRACTION99.35
2.76-2.840.29483370.22758180X-RAY DIFFRACTION98.39
2.84-2.920.26763410.2238307X-RAY DIFFRACTION99.84
2.92-3.020.27783440.20598355X-RAY DIFFRACTION99.85
3.02-3.120.25223420.20218305X-RAY DIFFRACTION99.65
3.12-3.250.24273450.20678350X-RAY DIFFRACTION99.64
3.25-3.40.24213420.20058338X-RAY DIFFRACTION99.72
3.4-3.580.21653450.18998379X-RAY DIFFRACTION99.65
3.58-3.80.24123400.18258290X-RAY DIFFRACTION98.57
3.8-4.090.19783470.16528413X-RAY DIFFRACTION99.95
4.09-4.510.1863480.15148454X-RAY DIFFRACTION99.77
4.51-5.160.19363470.15358458X-RAY DIFFRACTION99.53
5.16-6.490.21613490.1818445X-RAY DIFFRACTION98.36
6.49-49.810.193560.1668713X-RAY DIFFRACTION97.63
Refinement TLS params.Method: refined / Origin x: -47.7486482725 Å / Origin y: 55.698241923 Å / Origin z: -109.68559279 Å
111213212223313233
T0.289413029739 Å2-0.0393682695147 Å20.00912851418856 Å2-0.217364846894 Å20.00751778980813 Å2--0.29081886692 Å2
L0.132346202685 °2-0.0451069046977 °20.0335207929448 °2-0.0550313048989 °2-0.0475464559537 °2--0.11652221248 °2
S0.0134350400957 Å °0.0391935787651 Å °-0.0315777784696 Å °-0.0093812913063 Å °-0.00262661912988 Å °-0.0143103501562 Å °0.00486647143655 Å °-0.000713180652393 Å °-0.0089667340563 Å °
Refinement TLS groupSelection details: all

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