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- PDB-6w2z: Crystal Structure of the Beta Lactamase Class A PenP from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 6w2z
TitleCrystal Structure of the Beta Lactamase Class A PenP from Bacillus subtilis in the Complex with the Non-beta- lactam Beta-lactamase Inhibitor Avibactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase class A / Inhibitor / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic / extracellular region
Similarity search - Function
Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-NXL / Beta-lactamase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionMar 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8456
Polymers60,2022
Non-polymers6434
Water6,341352
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4143
Polymers30,1011
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4303
Polymers30,1011
Non-polymers3292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.681, 85.456, 70.360
Angle α, β, γ (deg.)90.000, 94.969, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-lactamase / Penicillinase


Mass: 30101.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: penP, BSU18800 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: P39824, beta-lactamase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 50 mM Bicine pH 8.8, 2.9 %(v/v), 25.7 %(w/v) PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 71543 / % possible obs: 95.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 3249 / CC1/2: 0.528 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6NI1

6ni1


Resolution: 1.5→27.1 Å / SU ML: 0.1782 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.3077
RfactorNum. reflection% reflection
Rfree0.1985 3521 4.93 %
Rwork0.1608 --
obs0.1627 71351 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.77 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 24 352 4414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614168
X-RAY DIFFRACTIONf_angle_d0.86375643
X-RAY DIFFRACTIONf_chiral_restr0.0789653
X-RAY DIFFRACTIONf_plane_restr0.0048723
X-RAY DIFFRACTIONf_dihedral_angle_d16.19781557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.28031180.24192116X-RAY DIFFRACTION75.24
1.52-1.540.29171220.23382663X-RAY DIFFRACTION92.52
1.54-1.560.23381290.2162730X-RAY DIFFRACTION95.52
1.56-1.590.26061530.21212698X-RAY DIFFRACTION94.69
1.59-1.610.27891450.19742725X-RAY DIFFRACTION96.21
1.61-1.640.24351310.17742780X-RAY DIFFRACTION96.23
1.64-1.670.23931440.17822721X-RAY DIFFRACTION95.76
1.67-1.70.25221400.1762753X-RAY DIFFRACTION96.43
1.7-1.740.25511440.17932725X-RAY DIFFRACTION95.6
1.74-1.770.24741410.18152744X-RAY DIFFRACTION96.1
1.77-1.810.2391360.17392766X-RAY DIFFRACTION95.4
1.81-1.860.23051250.16982748X-RAY DIFFRACTION96.25
1.86-1.910.221360.16162741X-RAY DIFFRACTION95.52
1.91-1.970.24541490.17032719X-RAY DIFFRACTION95.57
1.97-2.030.2041370.16592725X-RAY DIFFRACTION95.43
2.03-2.10.22851280.16082740X-RAY DIFFRACTION94.37
2.1-2.190.20971620.15472676X-RAY DIFFRACTION94.54
2.19-2.290.2131380.15672676X-RAY DIFFRACTION93.55
2.29-2.410.211480.15662661X-RAY DIFFRACTION92.92
2.41-2.560.20521570.15182628X-RAY DIFFRACTION92.99
2.56-2.750.19161520.16152727X-RAY DIFFRACTION94.89
2.75-3.030.19881440.17292800X-RAY DIFFRACTION96.87
3.03-3.470.18711390.16472847X-RAY DIFFRACTION99.1
3.47-4.370.16951560.13742871X-RAY DIFFRACTION98.99
4.37-27.10.15321470.14862850X-RAY DIFFRACTION97.12

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