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- PDB-3r4q: Crystal structure of Lactoylglutathione lyase from Agrobacterium ... -

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Basic information

Entry
Database: PDB / ID: 3r4q
TitleCrystal structure of Lactoylglutathione lyase from Agrobacterium tumefaciens
ComponentsLactoylglutathione lyase
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / ISOPROPYL ALCOHOL / Lactoylglutathione lyase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsAgarwal, R. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of Lactoylglutathione lyase from Agrobacterium tumefaciens
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
C: Lactoylglutathione lyase
D: Lactoylglutathione lyase
E: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6938
Polymers92,5145
Non-polymers1793
Water2,828157
1
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1855
Polymers37,0052
Non-polymers1793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-45 kcal/mol
Surface area12340 Å2
MethodPISA
2
C: Lactoylglutathione lyase
D: Lactoylglutathione lyase


Theoretical massNumber of molelcules
Total (without water)37,0052
Polymers37,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-35 kcal/mol
Surface area11900 Å2
MethodPISA
3
E: Lactoylglutathione lyase

E: Lactoylglutathione lyase


Theoretical massNumber of molelcules
Total (without water)37,0052
Polymers37,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4890 Å2
ΔGint-38 kcal/mol
Surface area11670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.530, 202.522, 50.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Lactoylglutathione lyase /


Mass: 18502.713 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_C_4259, Atu2344 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q7CXA0
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.02 Å3/Da / Density % sol: 39.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2010 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. all: 26390 / Num. obs: 26390 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 28.2 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4
Reflection shellResolution: 2.51→2.6 Å / Redundancy: 29 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5 / Num. unique all: 2600 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDSharpphasing
ARP/wARPmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.51→49.42 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 66876.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 744 2.9 %RANDOM
Rwork0.23 ---
obs0.23 25888 97.5 %-
all-26390 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.3256 Å2 / ksol: 0.336964 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å20 Å20 Å2
2---8.6 Å20 Å2
3---4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.51→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 9 157 5510
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.582.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.51→2.67 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 118 2.9 %
Rwork0.272 3971 -
obs-3971 94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramipa.top
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ipa.param

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