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- PDB-6v71: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica... -

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Basic information

Entry
Database: PDB / ID: 6v71
TitleCrystal Structure of Metallo Beta Lactamase from Hirschia baltica with Nitrate in the Active Site
ComponentsBeta-lactamase
KeywordsHYDROLASE / 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 superfamily / Metallo-beta-lactamase; Chain A / 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 superfamily / Metallo-beta-lactamase; Chain A / 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 / NITRATE ION / PHOSPHATE ION / beta-lactamase
Similarity search - Component
Biological speciesHirschia baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 with Nitrate in the Active Site
Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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)26,72620
Polymers25,5241
Non-polymers1,20219
Water2,810156
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,17860
Polymers76,5713
Non-polymers3,60757
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9660 Å2
ΔGint-219 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.362, 77.362, 241.321
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-319-

PO4

21A-319-

PO4

31A-533-

HOH

41A-550-

HOH

51A-552-

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, 175 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 4.0 M Sodium nitrate; 0.1M TRIS pH 8.5

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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: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.4→38.68 Å / Num. obs: 53220 / % possible obs: 96.3 % / Redundancy: 8.8 % / Biso Wilson estimate: 20.62 Å2 / Rsym value: 0.069 / Net I/σ(I): 35.2
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1991 / CC1/2: 0.788 / Rsym value: 0.611

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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: 1.4→38.68 Å / SU ML: 0.1087 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.3678
RfactorNum. reflection% reflection
Rfree0.1622 2628 4.94 %
Rwork0.1432 --
obs0.1441 53219 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.11 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 70 156 1885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151878
X-RAY DIFFRACTIONf_angle_d1.25282551
X-RAY DIFFRACTIONf_chiral_restr0.1017276
X-RAY DIFFRACTIONf_plane_restr0.0079342
X-RAY DIFFRACTIONf_dihedral_angle_d17.7503678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.21291010.18891996X-RAY DIFFRACTION72.86
1.43-1.450.17031060.15512309X-RAY DIFFRACTION83.83
1.45-1.480.18271420.1312585X-RAY DIFFRACTION95.08
1.48-1.510.16631390.11222655X-RAY DIFFRACTION97.49
1.51-1.550.13571470.10312675X-RAY DIFFRACTION97.75
1.55-1.590.13781590.09992649X-RAY DIFFRACTION97.74
1.59-1.630.14541300.10072680X-RAY DIFFRACTION97.98
1.63-1.680.16111500.10612701X-RAY DIFFRACTION97.84
1.68-1.730.13811430.10282680X-RAY DIFFRACTION98.36
1.73-1.80.13841270.10622729X-RAY DIFFRACTION98.55
1.8-1.870.13911450.10952698X-RAY DIFFRACTION98.75
1.87-1.950.14291250.11692742X-RAY DIFFRACTION98.9
1.95-2.060.151470.12482706X-RAY DIFFRACTION98.28
2.06-2.180.15611460.12842738X-RAY DIFFRACTION99.14
2.18-2.350.15241510.13322769X-RAY DIFFRACTION99.42
2.35-2.590.16911340.15032737X-RAY DIFFRACTION98.9
2.59-2.960.16391660.16342785X-RAY DIFFRACTION99.73
2.96-3.730.16921220.15792814X-RAY DIFFRACTION98.89
3.74-38.680.17391480.15962943X-RAY DIFFRACTION99.49

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