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- PDB-5kzh: High Resolution Structure of Acinetobacter baumannii beta-lactama... -

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Basic information

Entry
Database: PDB / ID: 5kzh
TitleHigh Resolution Structure of Acinetobacter baumannii beta-lactamase OXA-51
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic
Function / homology
Function and homology information


Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsJune, C.M. / Powers, R.A. / Leonard, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R15AI082416 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI094489 United States
CitationJournal: Protein Sci. / Year: 2016
Title: The structure of a doripenem-bound OXA-51 class D beta-lactamase variant with enhanced carbapenemase activity.
Authors: June, C.M. / Muckenthaler, T.J. / Schroder, E.C. / Klamer, Z.L. / Wawrzak, Z. / Powers, R.A. / Szarecka, A. / Leonard, D.A.
History
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,28216
Polymers112,6644
Non-polymers61712
Water20,2491124
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3635
Polymers28,1661
Non-polymers1974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3765
Polymers28,1661
Non-polymers2104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2713
Polymers28,1661
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2713
Polymers28,1661
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.549, 91.480, 169.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUILEILEAA36 - 27312 - 249
21GLUGLUILEILEBB36 - 27312 - 249
12ASPASPILEILEAA35 - 27311 - 249
22ASPASPILEILECC35 - 27311 - 249
13ASPASPLEULEUAA35 - 27411 - 250
23ASPASPLEULEUDD35 - 27411 - 250
14GLUGLUILEILEBB36 - 27312 - 249
24GLUGLUILEILECC36 - 27312 - 249
15GLUGLUILEILEBB36 - 27312 - 249
25GLUGLUILEILEDD36 - 27312 - 249
16ASPASPILEILECC35 - 27311 - 249
26ASPASPILEILEDD35 - 27311 - 249

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Beta-lactamase / Beta-lactamase OXA-51 / Class D beta-lactamase


Mass: 28166.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: oxa-51, blaOXA-51, AQ480_08190 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5QT35, beta-lactamase
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / Source method: isolated from a natural source / Formula: H2O
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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 3% w/v PGA-LM, 20% v/v PEG 500 MME, 0.1 M ammonium sulfate, 0.3 M sodium formate, and 0.1 M sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.08 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.61→42.31 Å / Num. obs: 176472 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.18
Reflection shellResolution: 1.61→1.65 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.51 / CC1/2: 0.783 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→42.31 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.579 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15796 8759 5 %RANDOM
Rwork0.11567 ---
obs0.11779 167336 99.37 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 23.379 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.61→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7549 0 41 1124 8714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.028038
X-RAY DIFFRACTIONr_bond_other_d0.0010.027700
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.95310928
X-RAY DIFFRACTIONr_angle_other_deg1.01317772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78151037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57725.515359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.302151418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5061529
X-RAY DIFFRACTIONr_chiral_restr0.1210.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.029249
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021834
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7471.9483958
X-RAY DIFFRACTIONr_mcbond_other3.7291.9443954
X-RAY DIFFRACTIONr_mcangle_it4.2132.9214967
X-RAY DIFFRACTIONr_mcangle_other4.2132.9214968
X-RAY DIFFRACTIONr_scbond_it5.5412.3184080
X-RAY DIFFRACTIONr_scbond_other5.5412.3194081
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2453.3335931
X-RAY DIFFRACTIONr_long_range_B_refined6.84825.5549865
X-RAY DIFFRACTIONr_long_range_B_other6.84625.5529863
X-RAY DIFFRACTIONr_rigid_bond_restr7.221315738
X-RAY DIFFRACTIONr_sphericity_free47.8885732
X-RAY DIFFRACTIONr_sphericity_bonded21.526515999
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A162500.1
12B162500.1
21A164520.07
22C164520.07
31A164340.09
32D164340.09
41B159520.09
42C159520.09
51B163500.07
52D163500.07
61C162280.08
62D162280.08
LS refinement shellResolution: 1.614→1.656 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 569 -
Rwork0.191 11772 -
obs--95.19 %

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