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- PDB-6wip: Class A beta-lactamase from Micromonospora aurantiaca ATCC 27029 -

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Basic information

Entry
Database: PDB / ID: 6wip
TitleClass A beta-lactamase from Micromonospora aurantiaca ATCC 27029
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / structural genomic / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / 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
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMicromonospora aurantiaca
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsChang, C. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: class A beta-lactamase from Micromonospora aurantiaca ATCC 27029
Authors: Chang, C. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)30,9437
Polymers30,4401
Non-polymers5026
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.115, 71.953, 100.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase


Mass: 30440.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora aurantiaca (strain ATCC 27029 / DSM 43813 / BCRC 12538 / CBS 129.76 / JCM 10878 / NBRC 16125 / NRRL B-16091 / INA 9442) (bacteria)
Strain: ATCC 27029 / DSM 43813 / BCRC 12538 / CBS 129.76 / JCM 10878 / NBRC 16125 / NRRL B-16091 / INA 9442
Gene: Micau_2858 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D9TA79, beta-lactamase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2M Ammonium sulfate, 0.1M MES, 30% PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 61376 / % possible obs: 97.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Χ2: 0.847 / Net I/σ(I): 6.5 / Num. measured all: 378050
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.424.90.53128730.8060.2530.5910.86192.4
1.42-1.4550.49529130.8090.2350.5510.84495.4
1.45-1.4850.47529980.8210.2290.5310.84296.5
1.48-1.515.40.41829630.8910.1940.4630.83596
1.51-1.546.10.40629990.9190.1790.4450.82696.6
1.54-1.586.30.3630420.940.1540.3920.83199.3
1.58-1.626.50.32430530.9470.1370.3520.8297.6
1.62-1.666.40.29530500.9560.1240.320.8297.9
1.66-1.716.30.24830680.9630.1060.2710.82499.6
1.71-1.765.90.21329890.9620.0940.2340.79196.5
1.76-1.836.70.19230840.9770.080.2090.80798.7
1.83-1.96.70.15730810.9810.0650.170.82698.8
1.9-1.996.70.12730600.9860.0530.1380.84698
1.99-2.096.50.09830930.9910.0410.1070.8599.3
2.09-2.226.10.07930900.9920.0340.0860.80798.3
2.22-2.396.70.07431470.9940.030.080.87699.3
2.39-2.636.80.06631380.9950.0270.0710.92899.7
2.63-3.026.50.05931950.9960.0250.0640.96799.9
3.02-3.86.30.04431730.9970.0190.0480.93998.7
3.8-506.20.03733670.9980.0160.0410.78799.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
SBC-Collectdata collection
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→41.25 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 15.25
RfactorNum. reflection% reflection
Rfree0.1632 5487 5.06 %
Rwork0.1397 --
obs0.1409 59501 90.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.69 Å2 / Biso mean: 17.9591 Å2 / Biso min: 6.47 Å2
Refinement stepCycle: final / Resolution: 1.4→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 28 408 2370
Biso mean--35.65 30.27 -
Num. residues----263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.410.21091160.17942166228258
1.41-1.430.20731250.17382344246962
1.43-1.450.20931430.17512570271368
1.45-1.470.19361710.17212650282171
1.47-1.490.20261560.16192642279870
1.49-1.510.18761560.16063027318380
1.51-1.530.18721550.1613202335785
1.53-1.550.19641880.15093311349988
1.55-1.580.17022140.14063430364492
1.58-1.60.17431740.13923512368692
1.6-1.630.15671890.14143566375595
1.63-1.660.15971790.13823663384295
1.66-1.690.16012010.13893632383398
1.69-1.720.19692140.15413677389196
1.72-1.760.1952050.14943490369593
1.76-1.80.19491740.14023685385997
1.8-1.850.16572100.13343769397999
1.85-1.90.18231920.13173701389398
1.9-1.950.17041980.13183672387097
1.95-2.020.14151960.13083699389599
2.02-2.090.15371740.12873761393599
2.09-2.170.1691870.12593783397099
2.17-2.270.1461990.12433645384496
2.27-2.390.15512120.12837924004100
2.39-2.540.14442030.127337573960100
2.54-2.740.14772210.141937453966100
2.74-3.010.17462030.148437643967100
3.01-3.450.15581740.13983713388798
3.45-4.340.14331850.128138053990100
4.35-41.250.16731730.1633737391098

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