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- PDB-2wym: Structure of a metallo-b-lactamase -

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Basic information

Entry
Database: PDB / ID: 2wym
TitleStructure of a metallo-b-lactamase
Components(L-ASCORBATE-6-PHOSPHATE LACTONASE ...) x 2
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
CITRATE ANION / : / Probable L-ascorbate-6-phosphate lactonase UlaG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)246,85020
Polymers245,6876
Non-polymers1,16314
Water3,477193
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32040 Å2
ΔGint-157.6 kcal/mol
Surface area58600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.221, 178.212, 111.559
Angle α, β, γ (deg.)90.00, 103.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

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L-ASCORBATE-6-PHOSPHATE LACTONASE ... , 2 types, 6 molecules ABDECF

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


Mass: 40938.445 Da / Num. of mol.: 4
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: Protein L-ASCORBATE-6-PHOSPHATE LACTONASE ULAG / METALLO-B-LACTAMASE / L-ASCORBATE UTILIZATION PROTEIN G


Mass: 40966.457 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 207 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.2M LITHIUM CITRATE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9788
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.6→24.5 Å / Num. obs: 60423 / % possible obs: 91.5 % / Observed criterion σ(I): 8.3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 3.19 / % possible all: 70.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WYL

2wyl


Resolution: 2.6→14.97 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 13.482 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3011 5 %RANDOM
Rwork0.207 ---
obs0.21 56646 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14454 0 61 193 14708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214962
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8681.91920325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09851788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92324.305727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.986152354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8361560
X-RAY DIFFRACTIONr_chiral_restr0.0610.22088
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211604
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.170.26991
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.29888
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2565
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2731.59191
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.494214433
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.36136818
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5964.55890
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: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 210 -
Rwork0.293 4570 -
obs--70.5 %

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