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- PDB-3g12: Crystal structure of a putative lactoylglutathione lyase from Bde... -

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Basic information

Entry
Database: PDB / ID: 3g12
TitleCrystal structure of a putative lactoylglutathione lyase from Bdellovibrio bacteriovorus
ComponentsPutative lactoylglutathione lyase
KeywordsLYASE / GLYOXALASE / BLEOMYCIN RESISTANCE / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / lyase activity / Roll / Alpha Beta / Putative lactoylglutathione lyase
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å
AuthorsPatskovsky, Y. / Madegowda, M. / Gilmore, M. / Chang, S. / Maletic, M. / Smith, D. / Sauder, J.M. / Burley, S.K. / Swaminathan, S. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative lactoylglutathione lyase from Bdellovibrio bacteriovorus
Authors: Patskovsky, Y. / Madegowda, M. / Gilmore, M. / Chang, S. / Maletic, M. / Smith, D. / Sauder, J.M. / Burley, S.K. / Swaminathan, S. / Almo, S.C.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative lactoylglutathione lyase
B: Putative lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6073
Polymers28,5112
Non-polymers961
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-15.4 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.276, 91.276, 57.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 117
2111B1 - 117

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Components

#1: Protein Putative lactoylglutathione lyase /


Mass: 14255.292 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Strain: HD100 / DSM 50701 / NCIB 9529 / Gene: Bd2520 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CODON+RIL / References: UniProt: Q6MK89
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Bis-tris pH 6.5, 2M Ammonium sulfate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 26, 2007
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 8394 / % possible obs: 99.8 % / Observed criterion σ(I): -5 / Redundancy: 4.5 % / Biso Wilson estimate: 49.658 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 5.4
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
SHELXDphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.58→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.252 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.862 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27481 231 2.9 %RANDOM
Rwork0.21211 ---
obs0.21392 7830 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 5 30 1775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221775
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9782404
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45125.34273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97515320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.905156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021288
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.140.3634
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.51177
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.5110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.349
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4521148
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.32831816
X-RAY DIFFRACTIONr_scbond_it5.5044683
X-RAY DIFFRACTIONr_scangle_it8.4197585
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 837 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.050.1
tight thermal0.231.5
LS refinement shellResolution: 2.58→2.646 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 22 -
Rwork0.306 546 -
obs--100 %

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