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- PDB-6v5m: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica... -

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Basic information

Entry
Database: PDB / ID: 6v5m
TitleCrystal Structure of Metallo Beta Lactamase from Hirschia baltica in Complex with Succinate
ComponentsBeta-lactamase
KeywordsHYDROLASE / metallo beta lactamase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich ...Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / SUCCINIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesHirschia baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMaltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica in Complex with Succinate.
Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,36211
Polymers25,5241
Non-polymers83810
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.609, 77.609, 241.883
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-554-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 25523.830 Da / Num. of mol.: 1 / Mutation: A257T / Source method: obtained synthetically
Source: (synth.) Hirschia baltica (strain ATCC 49814 / DSM 5838 / IFAM 1418) (bacteria)
References: UniProt: C6XID6, beta-lactamase

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Non-polymers , 6 types, 207 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M Succinic acid pH 7.0;0.1 M Bis-Tris Propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 31, 2017 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 45429 / % possible obs: 99.7 % / Redundancy: 14.1 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.138 / Net I/σ(I): 31.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2116 / CC1/2: 0.494 / Rsym value: 0.933 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V54

6v54


Resolution: 1.5→40.31 Å / SU ML: 0.1475 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.6231
RfactorNum. reflection% reflection
Rfree0.1674 2307 5.09 %
Rwork0.1416 --
obs0.143 45360 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.72 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 46 197 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071920
X-RAY DIFFRACTIONf_angle_d1.12852622
X-RAY DIFFRACTIONf_chiral_restr0.092289
X-RAY DIFFRACTIONf_plane_restr0.0076346
X-RAY DIFFRACTIONf_dihedral_angle_d22.7376700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.30581150.25382458X-RAY DIFFRACTION91.47
1.53-1.570.27341530.19282658X-RAY DIFFRACTION99.57
1.57-1.610.22891660.15742634X-RAY DIFFRACTION100
1.61-1.650.18641380.13042697X-RAY DIFFRACTION100
1.65-1.70.17261390.13022665X-RAY DIFFRACTION100
1.7-1.750.17671180.12052719X-RAY DIFFRACTION100
1.75-1.810.18191450.1172684X-RAY DIFFRACTION99.96
1.81-1.890.18541470.12062686X-RAY DIFFRACTION100
1.89-1.970.19281230.12452691X-RAY DIFFRACTION100
1.97-2.080.16921500.12652694X-RAY DIFFRACTION100
2.08-2.210.17791380.12512712X-RAY DIFFRACTION100
2.21-2.380.1741570.12452688X-RAY DIFFRACTION100
2.38-2.620.16481390.14392723X-RAY DIFFRACTION100
2.62-30.1621600.162724X-RAY DIFFRACTION99.93
3-3.770.16071450.14372762X-RAY DIFFRACTION100
3.77-40.310.14731740.14542858X-RAY DIFFRACTION99.9

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