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- PDB-5ypl: Crystal structure of NDM-1 bound to hydrolyzed imipenem represent... -

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Basic information

Entry
Database: PDB / ID: 5ypl
TitleCrystal structure of NDM-1 bound to hydrolyzed imipenem representing an EP complex
ComponentsMetallo-beta-lactamase NDM-1
KeywordsHYDROLASE / NDM-1 / Imipenem / EP complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HIW / Metallo-beta-lactamase type 2 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFeng, H. / Wang, D. / Liu, W.
CitationJournal: Nat Commun / Year: 2017
Title: The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis.
Authors: Feng, H. / Liu, X. / Wang, S. / Fleming, J. / Wang, D.C. / Liu, W.
History
DepositionNov 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase NDM-1
B: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,29210
Polymers51,2642
Non-polymers1,0288
Water6,684371
1
A: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1765
Polymers25,6321
Non-polymers5444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-10 kcal/mol
Surface area9790 Å2
MethodPISA
2
B: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1155
Polymers25,6321
Non-polymers4844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.220, 73.760, 77.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase NDM-1


Mass: 25631.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7Y424, UniProt: E5KIY2*PLUS

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Non-polymers , 5 types, 379 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HIW / (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid / Hydrolyzed Imipenem


Mass: 317.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O5S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 1.93 Å3/Da / Density % sol: 36.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 28% (w/v) PEG3350, 0.1M Bis-Tris, pH 5.8, 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 1.8→42.28 Å / Num. obs: 35229 / % possible obs: 94 % / Redundancy: 6.36 % / Rsym value: 0.07 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.44 % / Mean I/σ(I) obs: 2.55 / Rsym value: 0.555 / % possible all: 64.8

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RL0

4rl0


Resolution: 1.8→42.28 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.73
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2038 3792 5.68 %
Rwork0.1685 --
obs0.1705 35229 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 52 371 3825

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