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- PDB-6dmh: A multiconformer ligand model of acylenzyme intermediate of merop... -

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Basic information

Entry
Database: PDB / ID: 6dmh
TitleA multiconformer ligand model of acylenzyme intermediate of meropenem bound to an SFC-1 E166A mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Complex / multi conformer model / antibiotic / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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, 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
Chem-MER / beta-lactamase
Similarity search - Component
Biological speciesSerratia fonticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsHudson, B.M. / van Zundert, G. / Keedy, D.A. / Fonseca, R. / Heliou, A. / Suresh, P. / Borrelli, K. / Day, T. / Fraser, J.S. / van den Bedem, H.
Citation
Journal: J. Med. Chem. / Year: 2018
Title: qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
Authors: van Zundert, G.C.P. / Hudson, B.M. / de Oliveira, S.H.P. / Keedy, D.A. / Fonseca, R. / Heliou, A. / Suresh, P. / Borrelli, K. / Day, T. / Fraser, J.S. / van den Bedem, H.
#1: Journal: J. Am. Chem. Soc. / Year: 2012
Title: The basis for carbapenem hydrolysis by class A beta-lactamases: a combined investigation using crystallography and simulations.
Authors: Fonseca, F. / Chudyk, E.I. / van der Kamp, M.W. / Correia, A. / Mulholland, A.J. / Spencer, J.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _audit_author.name / _chem_comp.name ..._audit_author.name / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Remark 0THIS ENTRY 6DMH REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4EV4, DETERMINED BY F. ...THIS ENTRY 6DMH REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4EV4, DETERMINED BY F.FONSECA,E.I.CHUDYK,M.W.VAN DER KAMP,A.CORREIA,A.J.MULHOLLAND,J.SPENCER

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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)30,0516
Polymers29,4171
Non-polymers6345
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.185, 61.955, 79.127
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: 29417.150 Da / Num. of mol.: 1 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia fonticola (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6JP75, beta-lactamase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.12 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 4EV4
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Na acetate, PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 68435 / % possible obs: 94.7 % / Redundancy: 11.9 % / Net I/σ(I): 29.7
Reflection shellResolution: 1.3→1.35 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.3→33.345 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 12
RfactorNum. reflection% reflection
Rfree0.1426 1999 2.92 %
Rwork0.116 --
obs0.1167 68360 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 93.78 Å2 / Biso mean: 12.5936 Å2 / Biso min: 4.08 Å2
Refinement stepCycle: final / Resolution: 1.3→33.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 144 436 2647
Biso mean--14.32 28 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012386
X-RAY DIFFRACTIONf_angle_d1.373268
X-RAY DIFFRACTIONf_chiral_restr0.091364
X-RAY DIFFRACTIONf_plane_restr0.009430
X-RAY DIFFRACTIONf_dihedral_angle_d14.861915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2997-1.33220.1867950.13913160325564
1.3322-1.36820.16651320.11973818395077
1.3682-1.40850.14491110.10574413452488
1.4085-1.45390.13381560.09764678483495
1.4539-1.50590.12891510.09324903505499
1.5059-1.56620.13081410.090949755116100
1.5662-1.63750.12961440.091649775121100
1.6375-1.72380.14011530.097349865139100
1.7238-1.83180.13211500.107550045154100
1.8318-1.97320.151530.112949905143100
1.9732-2.17170.15511470.115450185165100
2.1717-2.48590.11981540.110950565210100
2.4859-3.13160.14261480.127950985246100
3.1316-33.35560.15391640.136352855449100

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