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- PDB-7o5q: Crystal Structure of a Class D Carbapenemase Complexed with Hydro... -

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Basic information

Entry
Database: PDB / ID: 7o5q
TitleCrystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / iodide / oxacillin
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-0WO / 1-BUTANOL / IODIDE ION / Chem-V3H / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZhou, Q. / He, Y. / Jin, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31400663 China
CitationJournal: To Be Published
Title: Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin
Authors: Zhou, Q. / He, Y. / Jin, Y.
History
DepositionApr 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Beta-lactamase
BBB: Beta-lactamase
CCC: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,13728
Polymers121,0174
Non-polymers4,12024
Water12,665703
1
AAA: Beta-lactamase
CCC: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,60414
Polymers60,5082
Non-polymers2,09512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,53314
Polymers60,5082
Non-polymers2,02512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.053, 126.902, 111.201
Angle α, β, γ (deg.)90.000, 98.289, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Beta-lactamase


Mass: 30254.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase

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Non-polymers , 6 types, 727 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-0WO / (2R,4S)-2-[(R)-carboxy{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carbo xylic acid / Oxacillin, hydroxylated form


Mass: 419.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#6: Chemical ChemComp-V3H / (2R,4S)-2-[(1R)-2-butoxy-1-[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonylamino]-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidin-3-ium-4-carboxylic acid / Hydrolyzed Oxacillin


Mass: 476.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30N3O6S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 8.0, 10% PEG 8000, 10% 1-BUTANOL mixed with the 10 mg/mL protein stock at 1:1 ratio.
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→19.81 Å / Num. obs: 109814 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 10
Reflection shellResolution: 1.85→1.88 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5493 / CC1/2: 0.725

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p


Resolution: 1.85→19.807 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.851 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2111 5465 4.978 %
Rwork0.1731 104317 -
all0.175 --
obs-109782 99.864 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.894 Å2
Baniso -1Baniso -2Baniso -3
1-3.963 Å20 Å20.53 Å2
2---2.548 Å2-0 Å2
3----1.505 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 167 703 8802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138372
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187798
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.63811344
X-RAY DIFFRACTIONr_angle_other_deg1.311.58517885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16422.735479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.699151436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4421549
X-RAY DIFFRACTIONr_chiral_restr0.0810.21048
X-RAY DIFFRACTIONr_chiral_restr_other0.090.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022087
X-RAY DIFFRACTIONr_nbd_refined0.2050.21319
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.26223
X-RAY DIFFRACTIONr_nbtor_refined0.1580.23801
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2398
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.27
X-RAY DIFFRACTIONr_nbd_other0.2970.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.217
X-RAY DIFFRACTIONr_mcbond_it2.112.6593924
X-RAY DIFFRACTIONr_mcbond_other2.1092.663925
X-RAY DIFFRACTIONr_mcangle_it2.923.9694912
X-RAY DIFFRACTIONr_mcangle_other2.9193.9694912
X-RAY DIFFRACTIONr_scbond_it3.0923.0774448
X-RAY DIFFRACTIONr_scbond_other3.0923.0774449
X-RAY DIFFRACTIONr_scangle_it4.7754.486432
X-RAY DIFFRACTIONr_scangle_other4.7754.486433
X-RAY DIFFRACTIONr_lrange_it5.85830.6769119
X-RAY DIFFRACTIONr_lrange_other5.77830.2778982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.3633870.3727755X-RAY DIFFRACTION99.8651
1.898-1.950.3274080.3287499X-RAY DIFFRACTION100
1.95-2.0070.2973580.287255X-RAY DIFFRACTION99.9869
2.007-2.0680.2583580.2327095X-RAY DIFFRACTION100
2.068-2.1360.2673690.2136976X-RAY DIFFRACTION100
2.136-2.2110.2433390.1916591X-RAY DIFFRACTION100
2.211-2.2940.2043430.1736390X-RAY DIFFRACTION100
2.294-2.3880.2023130.1616199X-RAY DIFFRACTION99.9846
2.388-2.4940.2083400.1595920X-RAY DIFFRACTION100
2.494-2.6160.1982830.155681X-RAY DIFFRACTION100
2.616-2.7570.2023010.1485411X-RAY DIFFRACTION100
2.757-2.9250.1812850.1455060X-RAY DIFFRACTION100
2.925-3.1260.2012480.164795X-RAY DIFFRACTION100
3.126-3.3770.2022230.1624494X-RAY DIFFRACTION100
3.377-3.6990.1952280.1534088X-RAY DIFFRACTION100
3.699-4.1350.1741990.143698X-RAY DIFFRACTION99.9743
4.135-4.7740.1681500.1233348X-RAY DIFFRACTION100
4.774-5.8440.1991520.152786X-RAY DIFFRACTION100
5.844-8.2570.2221220.1812142X-RAY DIFFRACTION100

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