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- PDB-2wyl: Apo structure of a metallo-b-lactamase -

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Basic information

Entry
Database: PDB / ID: 2wyl
TitleApo structure of a metallo-b-lactamase
ComponentsL-ASCORBATE-6-PHOSPHATE LACTONASE ULAG
KeywordsHYDROLASE
Function / homology
Function and homology information


L-ascorbate 6-phosphate lactonase activity / L-ascorbic acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / manganese ion binding / hydrolase activity / cytoplasm
Similarity search - Function
L-ascorbate-6-phosphate lactonase UlaG / : / Beta-lactamase superfamily domain / : / Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMYL GROUP / Probable L-ascorbate-6-phosphate lactonase UlaG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsGarces, F. / Fernandez, F.J. / Penya-Soler, E. / Aguilar, J. / Baldoma, L. / Coll, M. / Badia, J. / Vega, M.C.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Molecular Architecture of the Mn(2+)Dependent Lactonase Ulag Reveals an Rnase-Like Metallo-Beta-Lactamase Fold and a Novel Quaternary Structure.
Authors: Garces, F. / Fernandez, F.J. / Montella, C. / Penya-Soler, E. / Prohens, R. / Aguilar, J. / Baldoma, L. / Coll, M. / Badia, J. / Vega, M.C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Overproduction, Crystallization and Preliminary X-Ray Analysis of the Putative L-Ascorbate-6-Phosphate Lactonase Ulag from Escherichia Coli.
Authors: Garces, F. / Fernandez, F.J. / Perez-Luque, R. / Aguilar, J. / Baldoma, L. / Coll, M. / Badia, J. / Vega, M.C.
History
DepositionNov 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG
B: L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG
C: L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG
D: L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG
E: L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG
F: L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,62828
Polymers248,7266
Non-polymers1,90222
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34720 Å2
ΔGint-117.2 kcal/mol
Surface area59140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.610, 178.560, 112.420
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG / METALLO-B-LACTAMASE / L-ASCORBATE UTILIZATION PROTEIN G


Mass: 41454.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P39300, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 200 MM LITHIUM CITRATE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.59→24.79 Å / Num. obs: 60575 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 8.9 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.3
Reflection shellResolution: 2.59→2.73 Å / Redundancy: 8.6 % / % possible all: 74

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.59→14.94 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.613 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3037 5 %RANDOM
Rwork0.198 ---
obs0.201 57221 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.59→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14520 0 124 382 15026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02215084
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.92220460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.90651797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06524.219730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.577152386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2551565
X-RAY DIFFRACTIONr_chiral_restr0.0610.22097
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211637
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1690.26742
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.29839
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2687
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3361.59245
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.525214485
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.44936913
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.694.55972
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 177 -
Rwork0.305 7831 -
obs--83.08 %

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