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- PDB-6v54: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica -

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Basic information

Entry
Database: PDB / ID: 6v54
TitleCrystal Structure of Metallo Beta Lactamase from Hirschia baltica
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 / beta-lactamase
Similarity search - Component
Biological speciesHirschia baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 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.
Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A.
History
DepositionDec 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_symmetry

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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)26,38110
Polymers25,8521
Non-polymers5299
Water3,369187
1
A: Beta-lactamase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)158,28660
Polymers155,1136
Non-polymers3,17354
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area16310 Å2
ΔGint-581 kcal/mol
Surface area48330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.668, 77.668, 240.998
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-301-

MG

21A-511-

HOH

31A-539-

HOH

41A-545-

HOH

51A-555-

HOH

61A-581-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 25852.098 Da / Num. of mol.: 1 / Mutation: A257T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirschia baltica (strain ATCC 49814 / DSM 5838 / IFAM 1418) (bacteria)
Strain: ATCC 49814 / DSM 5838 / IFAM 1418 / Gene: Hbal_3075 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: C6XID6, beta-lactamase

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Non-polymers , 7 types, 196 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 8000, 0.1M TRIS pH 7.0, 0.2M magnesium chloride

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→29.37 Å / Num. obs: 49632 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.03 Å2 / Rsym value: 0.09 / Net I/σ(I): 18.4
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2422 / CC1/2: 0.505 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→29.37 Å / SU ML: 0.123 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.3716
RfactorNum. reflection% reflection
Rfree0.1625 2460 4.96 %
Rwork0.1324 --
obs0.1338 49548 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.02 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 9 187 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01371896
X-RAY DIFFRACTIONf_angle_d1.29612590
X-RAY DIFFRACTIONf_chiral_restr0.0991281
X-RAY DIFFRACTIONf_plane_restr0.0092345
X-RAY DIFFRACTIONf_dihedral_angle_d19.0534706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.23631190.212414X-RAY DIFFRACTION92.21
1.48-1.510.25581430.17742613X-RAY DIFFRACTION99.17
1.51-1.540.20051490.1472584X-RAY DIFFRACTION99.85
1.54-1.580.18931600.13392582X-RAY DIFFRACTION99.96
1.58-1.620.17581470.1282625X-RAY DIFFRACTION100
1.62-1.660.1661310.11442610X-RAY DIFFRACTION99.96
1.66-1.710.16321420.10732624X-RAY DIFFRACTION99.96
1.71-1.760.1371200.1082650X-RAY DIFFRACTION99.89
1.76-1.830.14351470.10532606X-RAY DIFFRACTION99.85
1.83-1.90.15061230.10662648X-RAY DIFFRACTION99.75
1.9-1.990.16281470.11262634X-RAY DIFFRACTION99.71
1.99-2.090.14741330.11562643X-RAY DIFFRACTION99.57
2.09-2.220.1481330.11812630X-RAY DIFFRACTION99.32
2.22-2.390.16321300.12482626X-RAY DIFFRACTION99.14
2.39-2.630.17221280.13582645X-RAY DIFFRACTION98.89
2.63-3.010.14221210.1442661X-RAY DIFFRACTION98.3
3.01-3.790.16011460.13662631X-RAY DIFFRACTION97.64
3.8-29.370.16791410.14922662X-RAY DIFFRACTION94.06

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