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- PDB-6v61: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica... -

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Basic information

Entry
Database: PDB / ID: 6v61
TitleCrystal Structure of Metallo Beta Lactamase from Hirschia baltica in the Complex with the Inhibitor Captopril
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 / L-CAPTOPRIL / beta-lactamase
Similarity search - Component
Biological speciesHirschia baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 the Complex with the Inhibitor Captopril.
Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A.
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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,21413
Polymers25,5241
Non-polymers69012
Water3,045169
1
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,64239
Polymers76,5713
Non-polymers2,07036
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area5850 Å2
ΔGint-141 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.893, 77.893, 241.426
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-311-

CL

21A-480-

HOH

31A-492-

HOH

41A-540-

HOH

51A-563-

HOH

61A-568-

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 , 7 types, 181 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-X8Z / L-CAPTOPRIL


Mass: 217.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2M Sodium chloride; 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: 0.9791 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 38932 / % possible obs: 99.2 % / Redundancy: 8.9 % / Biso Wilson estimate: 22.26 Å2 / Rsym value: 0.051 / Net I/σ(I): 40.24
Reflection shellResolution: 1.58→1.61 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1637 / CC1/2: 0.913 / Rsym value: 0.449

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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: 1.58→44.98 Å / SU ML: 0.1537 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.8825
RfactorNum. reflection% reflection
Rfree0.1952 1949 5.01 %
Rwork0.1665 --
obs0.1679 38929 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.26 Å2
Refinement stepCycle: LAST / Resolution: 1.58→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 32 169 1874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791816
X-RAY DIFFRACTIONf_angle_d0.94462479
X-RAY DIFFRACTIONf_chiral_restr0.0641275
X-RAY DIFFRACTIONf_plane_restr0.006327
X-RAY DIFFRACTIONf_dihedral_angle_d19.3125663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.24651260.20052547X-RAY DIFFRACTION97.63
1.62-1.670.20541520.17652587X-RAY DIFFRACTION100
1.67-1.710.19681440.16712625X-RAY DIFFRACTION100
1.71-1.770.20151310.16872627X-RAY DIFFRACTION99.96
1.77-1.830.19021450.16362594X-RAY DIFFRACTION99.89
1.83-1.910.21591400.16652632X-RAY DIFFRACTION100
1.91-1.990.18631650.16942604X-RAY DIFFRACTION100
1.99-2.10.20051270.16762632X-RAY DIFFRACTION100
2.1-2.230.20091390.16282619X-RAY DIFFRACTION99.82
2.23-2.40.18871270.17052642X-RAY DIFFRACTION99.96
2.4-2.640.21151520.17372658X-RAY DIFFRACTION100
2.64-3.030.19891150.17982697X-RAY DIFFRACTION99.96
3.03-3.810.2011420.1642693X-RAY DIFFRACTION99.96
3.81-44.980.17671440.15582823X-RAY DIFFRACTION99.87
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)
11.36372059804-0.01893071165160.0299815203614.075182650881.506515263593.10062888138-0.0447230349091-0.158514210031-0.1410383301710.229889204708-0.02574065923790.2297728823070.1557843114170.1882025897270.06373842516410.1851876787440.04764952899990.04911853802520.2710230361970.05720778389150.20186088778-19.7405346946-35.4136958003-11.5352149188
22.69655689921-0.315995107444-1.294056631611.83991859715-0.1232644160262.93007825517-0.02738160179350.109686210685-0.00747914926788-0.0566852808560.001672962319760.179446247467-0.1544803059460.0296612522220.02376598432490.145500427093-0.00099903925604-0.01431917355730.1817583071240.01102359807480.172731700392-25.3591616228-27.9009313341-20.4847450057
32.22309936395-0.195637900306-0.4427736409242.711146273491.099279303523.88359295904-0.03941167529140.0784277636543-0.130367780446-0.06202850246120.0428934148867-0.09623567349630.0004279178774570.4388223961090.006794923659430.149749205727-0.0418942208278-0.006620138090960.3331461318060.03398358676170.171429400381-10.1451353766-31.1800427248-25.7120337626
41.7625877519-0.618286071126-0.1614999149773.489442346260.912330178771.16268623711-0.0628814285255-0.1331366245480.0469573970411-0.09528865900150.0825442314999-0.197844173606-0.06140293241930.777521522959-0.03920779586480.15785752913-0.022579508589-0.007091316394430.4756648639790.02577432551410.16213233509-5.2579956316-32.2600717482-21.6467648083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 259 )

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