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- PDB-5aeb: Crystal structure of the class B3 di-zinc metallo-beta-lactamase ... -

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Basic information

Entry
Database: PDB / ID: 5aeb
TitleCrystal structure of the class B3 di-zinc metallo-beta-lactamase LRA- 12 from an Alaskan soil metagenome.
ComponentsLRA-12
KeywordsHYDROLASE / MBL / CARBAPENEMASE / METAGENOMICS / CARBAPENEM-RESISTANCE / ENVIRONMENTAL RESISTOME
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / 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
Biological speciesUNCULTURED BACTERIUM BLR12 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPower, P. / Herman, R. / Kerff, F. / Bouillenne, F. / Rodriguez, M.M. / Galleni, M. / Handelsman, J. / Gutkind, G. / Charlier, P. / Sauvage, E.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structure and kinetic analysis of the class B3 di-zinc metallo-beta-lactamase LRA-12 from an Alaskan soil metagenome.
Authors: Rodriguez, M.M. / Herman, R. / Ghiglione, B. / Kerff, F. / D'Amico Gonzalez, G. / Bouillenne, F. / Galleni, M. / Handelsman, J. / Charlier, P. / Gutkind, G. / Sauvage, E. / Power, P.
History
DepositionAug 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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_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: LRA-12
B: LRA-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,62212
Polymers60,8212
Non-polymers80110
Water4,179232
1
A: LRA-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7936
Polymers30,4111
Non-polymers3825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LRA-12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8306
Polymers30,4111
Non-polymers4195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.148, 80.616, 78.288
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LRA-12 / METALLO-BETA-LACTAMASE


Mass: 30410.639 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 26-293 / Source method: isolated from a natural source
Details: METAGENOMIC-DERIVED BETA-LACTAMASE FROM ALASKAN SOIL
Source: (natural) UNCULTURED BACTERIUM BLR12 (environmental samples)
References: UniProt: B5L5V5, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.37 Å3/Da / Density % sol: 47.8 % / Description: NONE
Crystal growDetails: 25% PEG 3350, 0.1M TRIS (PH 8.5), 0.2 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→46.59 Å / Num. obs: 33531 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.3 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JT1

1jt1
PDB Unreleased entry


Resolution: 2.1→42.93 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.897 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 1697 5.1 %RANDOM
Rwork0.18448 ---
obs0.18707 31806 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.509 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4160 0 30 232 4422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024274
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9595765
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20524.645183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90415762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.6621512
X-RAY DIFFRACTIONr_chiral_restr0.1020.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213160
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 123 -
Rwork0.245 2275 -
obs--97.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.20320.52010.04580.8124-0.18661.1076-0.0172-0.03750.0266-0.0837-0.0579-0.09480.26440.05010.07510.26210.01150.01380.1896-0.0040.203611.0161-15.039221.2329
20.0428-0.16640.04531.2405-0.14250.77570.00640.07770.0012-0.1228-0.0790.00710.21890.01820.07260.2168-0.00180.01430.2519-0.03550.21149.2404-10.663914.9968
30.30810.0705-0.30161.2270.14361.9679-0.02570.04870.111-0.0355-0.0815-0.046-0.18930.13540.10720.2116-0.01070.01140.19750.03750.209812.84692.56616.6055
42.40320.94680.63170.90510.17611.6371-0.04310.04110.05610.1285-0.031-0.0267-0.0844-0.0090.07410.22820.00570.00170.1870.00590.20249.5296-0.284130.7326
50.8272-0.1293-0.32650.5554-0.72421.6984-0.0312-0.0327-0.0577-0.00310.0368-0.03960.2899-0.104-0.00560.2765-0.02930.0120.20380.01660.19436.5613-14.425134.403
610.68326.8329-1.34476.2768-2.41761.610.1447-0.2789-0.04880.4977-0.3217-0.1819-0.13950.27080.1770.39110.0526-0.02610.26610.04730.122519.6923-2.248241.5764
71.1301-0.01130.37780.58540.07341.3975-0.0379-0.0050.02130.03960.0136-0.0504-0.1067-0.17910.02430.18760.00720.03430.21070.00120.2245-14.416131.893919.4314
81.0928-0.21910.05230.3353-0.18440.8339-0.037-0.062-0.06080.04770.0215-0.01270.0535-0.03970.01560.2116-0.00310.01180.1866-0.00420.2038-7.972623.55723.9179
92.06380.38540.58251.1120.40730.93410.06340.1291-0.1347-0.0344-0.1040.04210.1505-0.15710.04070.23280.01020.03470.2099-0.0170.2143-6.404522.21629.0025
104.42770.41292.2750.5940.54622.9544-0.0348-0.07730.2198-0.0281-0.0493-0.0454-0.11750.15270.0840.19750.00320.03360.17930.0210.21616.345932.159113.6671
111.24260.33020.08710.8447-0.46671.3070.0220.1480.1261-0.05860.0040.0448-0.1265-0.1766-0.0260.21520.00860.00440.20780.01970.2027-10.559234.97535.0571
1219.78791.852313.6686.5969-3.08612.4182-0.09510.42251.01730.5775-0.46790.0979-0.44420.57370.56310.3924-0.10040.21210.09310.07360.36928.983241.775710.661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 78
2X-RAY DIFFRACTION2A79 - 127
3X-RAY DIFFRACTION3A128 - 181
4X-RAY DIFFRACTION4A182 - 249
5X-RAY DIFFRACTION5A250 - 290
6X-RAY DIFFRACTION6A291 - 306
7X-RAY DIFFRACTION7B26 - 78
8X-RAY DIFFRACTION8B79 - 183
9X-RAY DIFFRACTION9B184 - 212
10X-RAY DIFFRACTION10B213 - 251
11X-RAY DIFFRACTION11B252 - 294
12X-RAY DIFFRACTION12B295 - 306

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