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- PDB-2p25: The crystal structure of the glyoxalase family protein from Enter... -

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Basic information

Entry
Database: PDB / ID: 2p25
TitleThe crystal structure of the glyoxalase family protein from Enterococcus faecalis
ComponentsGlyoxalase family protein
KeywordsOXIDOREDUCTASE / glyoxalase / structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


YwkD-like domain / : / 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
Glyoxylase family protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsZhang, R. / Wu, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the glyoxalase family protein from Enterococcus faecalis
Authors: Zhang, R. / Wu, R. / Moy, S. / Joachimiak, A.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)14,8321
Polymers14,8321
Non-polymers00
Water2,432135
1
A: Glyoxalase family protein

A: Glyoxalase family protein


Theoretical massNumber of molelcules
Total (without water)29,6652
Polymers29,6652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5550 Å2
ΔGint-41 kcal/mol
Surface area12120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.695, 67.893, 87.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThis protein existed as dimer, the second part of the biological assembly is generated by the two fold axis: X, -Y+1, -Z+1

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Components

#1: Protein Glyoxalase family protein


Mass: 14832.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_2214 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q832L2, lactoylglutathione lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.1M di-Ammonium Tartrate, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2007 / Details: mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.7→43.77 Å / Num. all: 16151 / Num. obs: 15655 / % possible obs: 96.93 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 26.92
Reflection shellResolution: 1.7→1.742 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3 / % possible all: 95.18

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→43.77 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.756 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.11
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22958 831 5 %RANDOM
Rwork0.20075 ---
all0.20212 15615 --
obs0.20212 15615 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---0.92 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.043 Å0.04 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 1.7→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 135 1177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9561460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4845127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06824.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87815190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.537155
X-RAY DIFFRACTIONr_chiral_restr0.1310.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02843
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2433
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2736
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2841.5653
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77721030
X-RAY DIFFRACTIONr_scbond_it2.8213467
X-RAY DIFFRACTIONr_scangle_it4.1074.5430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 55 -
Rwork0.238 1091 -
obs--95.18 %
Refinement TLS params.Method: refined / Origin x: 22.288 Å / Origin y: 40.796 Å / Origin z: 39.27 Å
111213212223313233
T-0.0524 Å2-0.0112 Å20.0034 Å2--0.0197 Å20.0072 Å2---0.0115 Å2
L0.5458 °20.2198 °2-0.0205 °2-1.2631 °20.1253 °2--0.7627 °2
S-0.0224 Å °0.0482 Å °-0.0039 Å °-0.0326 Å °0.014 Å °-0.1358 Å °-0.0816 Å °0.0543 Å °0.0084 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 301 - 30
2X-RAY DIFFRACTION1AA31 - 6031 - 60
3X-RAY DIFFRACTION1AA61 - 9061 - 90
4X-RAY DIFFRACTION1AA91 - 12691 - 126

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