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- PDB-2qjs: Stenotrophomonas maltophilia L1 metallo-beta-lactamase Asp-120 As... -

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Basic information

Entry
Database: PDB / ID: 2qjs
TitleStenotrophomonas maltophilia L1 metallo-beta-lactamase Asp-120 Asn mutant
ComponentsMetallo-beta-lactamase L1
KeywordsHYDROLASE / metallo-beta-lactamase / dinculear / binculear
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCrisp, J. / Conners, R. / Spencer, J.
Citation
Journal: Biochemistry / Year: 2007
Title: Structural Basis for the Role of Asp-120 in Metallo-beta-lactamases
Authors: Crisp, J. / Conners, R. / Garrity, J.D. / Carenbauer, A.L. / Crowder, M.W. / Spencer, J.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Metal Binding Asp-120 in Metallo-beta-lactamase L1 from Stenotrophomonas maltophilia Plays a Crucial Role in Catalysis
Authors: Garrity, J.D. / Carenbauer, A.L. / Herron, L.R. / Crowder, M.W.
History
DepositionJul 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase L1
B: Metallo-beta-lactamase L1
C: Metallo-beta-lactamase L1
D: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,48112
Polymers114,9584
Non-polymers5238
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8703
Polymers28,7391
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8703
Polymers28,7391
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8703
Polymers28,7391
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Metallo-beta-lactamase L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8703
Polymers28,7391
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.382, 86.382, 227.363
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Metallo-beta-lactamase L1 / Beta-lactamase type II / Penicillinase


Mass: 28739.469 Da / Num. of mol.: 4 / Mutation: D120N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: IID 1275 / Gene: L1 / Plasmid: pUB5832 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P52700, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris.Cl pH 8.0, 0.4M MgCl2, 21% PEG 4000, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 47690 / Num. obs: 47129 / % possible obs: 98.8 % / Redundancy: 4.4 % / Biso Wilson estimate: 52.856 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.026 / Net I/σ(I): 12.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4559 / Χ2: 1.025 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SML

1sml


Resolution: 2.25→10 Å / Num. parameters: 31284 / Num. restraintsaints: 31022 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflectionSelection details
Rfree0.2827 2325 RANDOM
all0.2532 46962 -
obs-44239 -
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7810
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7416 0 8 396 7820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0224
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.09
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0

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