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- PDB-8i08: Crystal structure of Escherichia coli glyoxylate carboligase quad... -

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Basic information

Entry
Database: PDB / ID: 8i08
TitleCrystal structure of Escherichia coli glyoxylate carboligase quadruple 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 / L-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 / L-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: 1.91 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

Downloads & links

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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
Water68,7813818
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 area31910 Å2
ΔGint-247 kcal/mol
Surface area65710 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 area32210 Å2
ΔGint-241 kcal/mol
Surface area64940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.565, 188.565, 246.486
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

21A-1232-

HOH

31B-1327-

HOH

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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, L478M, R484M, M488L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: gcl / 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, 3852 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.: 3818 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
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: Oct 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 337289 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 19.05 Å2 / Rmerge(I) obs: 0.989 / Χ2: 0.089 / Net I/σ(I): 2.1 / Num. measured all: 4914883
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.91-1.945.50.964326080.33199.3
1.94-1.985.80.957325750.326199.5
1.98-2.026.10.924326660.33199.5
2.02-2.066.30.891326590.339199.7
2.06-2.16.50.855326740.35199.7
2.1-2.156.50.795327440.36199.7
2.15-2.26.10.743325880.36199.5
2.2-2.266.90.698327420.395199.6
2.26-2.337.20.661326460.394199.7
2.33-2.417.30.595326550.414199.6
2.41-2.497.30.542326030.443199.5
2.49-2.597.30.469325690.485199.4
2.59-2.716.80.417326370.501199.5
2.71-2.8580.365326670.548199.5
2.85-3.038.10.302325930.631199.5
3.03-3.278.30.243327180.747199.7
3.27-3.598.30.183327230.948199.8
3.59-4.119.80.144327291.096199.8
4.11-5.18100.11327291.191199.8
5.18-5012.20.074328370.8131100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXv2.0refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→49.92 Å / SU ML: 0.305 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2717 9986 2.96 %
Rwork0.2254 326923 -
obs0.2268 336909 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.27 Å2
Refinement stepCycle: LAST / Resolution: 1.91→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27239 0 640 3818 31697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007728457
X-RAY DIFFRACTIONf_angle_d0.995538705
X-RAY DIFFRACTIONf_chiral_restr0.06114314
X-RAY DIFFRACTIONf_plane_restr0.01014992
X-RAY DIFFRACTIONf_dihedral_angle_d15.94510331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.930.38923160.384410336X-RAY DIFFRACTION95.09
1.93-1.960.38253300.376210804X-RAY DIFFRACTION99.54
1.96-1.980.39253300.373610822X-RAY DIFFRACTION99.7
1.98-2.010.35863320.363410835X-RAY DIFFRACTION99.53
2.01-2.030.36523300.356410784X-RAY DIFFRACTION99.78
2.03-2.060.35733300.352510800X-RAY DIFFRACTION99.67
2.06-2.090.38453310.347710868X-RAY DIFFRACTION99.7
2.09-2.120.35613320.329910872X-RAY DIFFRACTION99.89
2.12-2.150.34523310.318110845X-RAY DIFFRACTION99.75
2.15-2.190.33033310.307810820X-RAY DIFFRACTION99.67
2.19-2.230.33813310.295310853X-RAY DIFFRACTION99.71
2.23-2.270.36543320.289310870X-RAY DIFFRACTION99.74
2.27-2.310.30573310.27210822X-RAY DIFFRACTION99.72
2.31-2.360.29763340.264610913X-RAY DIFFRACTION99.71
2.36-2.410.32083310.257910825X-RAY DIFFRACTION99.6
2.41-2.460.28553320.246810866X-RAY DIFFRACTION99.49
2.46-2.530.28833320.241410863X-RAY DIFFRACTION99.53
2.53-2.590.29583310.229410855X-RAY DIFFRACTION99.4
2.59-2.670.27963320.224510876X-RAY DIFFRACTION99.63
2.67-2.760.27953320.216110881X-RAY DIFFRACTION99.49
2.76-2.860.25083340.195310904X-RAY DIFFRACTION99.5
2.86-2.970.24343320.190810903X-RAY DIFFRACTION99.52
2.97-3.110.26093330.187610954X-RAY DIFFRACTION99.62
3.11-3.270.22583330.173410927X-RAY DIFFRACTION99.62
3.27-3.470.22883370.160610987X-RAY DIFFRACTION99.64
3.47-3.740.2333370.156111010X-RAY DIFFRACTION99.75
3.74-4.120.17763370.139611066X-RAY DIFFRACTION99.89
4.12-4.710.19933380.13811086X-RAY DIFFRACTION99.43
4.71-5.940.2073410.15911195X-RAY DIFFRACTION99.7
5.94-49.920.20873530.174411481X-RAY DIFFRACTION98.65
Refinement TLS params.Method: refined / Origin x: -47.5326656329 Å / Origin y: 55.8064711339 Å / Origin z: -109.266986153 Å
111213212223313233
T0.185745994608 Å2-0.0139154664093 Å2-0.00417283380777 Å2-0.154413426895 Å20.00255787136035 Å2--0.185544109054 Å2
L0.0601197366062 °2-0.0267182992848 °20.0235818861151 °2-0.0773772420304 °2-0.0588741064069 °2--0.0418912455492 °2
S0.0315900177253 Å °0.0844084279706 Å °-0.0465435995573 Å °-0.0673832339327 Å °-0.0210248845784 Å °0.00186624642316 Å °0.0200506934762 Å °0.0076167201973 Å °-0.00901559288181 Å °
Refinement TLS groupSelection details: all

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