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

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Basic information

Entry
Database: PDB / ID: 5ypk
TitleCrystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI2 complex
ComponentsMetallo-beta-lactamase NDM-1
KeywordsHYDROLASE / NDM-1 / Imipenem / EI2 complex
Function / homology
Function and homology information


antibiotic catabolic process / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Beta
Similarity search - Domain/homology
Chem-HIW / Metallo-beta-lactamase NDM-1 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1May 16, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase NDM-1
B: Metallo-beta-lactamase NDM-1
C: Metallo-beta-lactamase NDM-1
D: Metallo-beta-lactamase NDM-1
E: Metallo-beta-lactamase NDM-1
F: Metallo-beta-lactamase NDM-1
G: Metallo-beta-lactamase NDM-1
H: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,50947
Polymers205,0558
Non-polymers4,45439
Water34,4271911
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 area170 Å2
ΔGint-12 kcal/mol
Surface area9690 Å2
MethodPISA
2
B: 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 area0 Å2
ΔGint0 kcal/mol
Surface area9550 Å2
MethodPISA
3
C: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3188
Polymers25,6321
Non-polymers6867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9610 Å2
MethodPISA
4
E: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1996
Polymers25,6321
Non-polymers5675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9610 Å2
MethodPISA
5
F: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1996
Polymers25,6321
Non-polymers5675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9610 Å2
MethodPISA
6
G: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1035
Polymers25,6321
Non-polymers4714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9630 Å2
MethodPISA
7
H: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0804
Polymers25,6321
Non-polymers4483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9640 Å2
MethodPISA
8
D: Metallo-beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2578
Polymers25,6321
Non-polymers6267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.240, 73.610, 154.520
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 25631.820 Da / Num. of mol.: 8
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 , 6 types, 1950 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / 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.: 8 / Source method: obtained synthetically / Formula: C12H19N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1911 / 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: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 28% (w/v) PEG 3350, 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: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→42.212 Å / Num. obs: 100028 / % possible obs: 90 % / Redundancy: 1.73 % / Rsym value: 0.072 / Net I/σ(I): 8.65
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.37 % / Mean I/σ(I) obs: 2.06 / Rsym value: 0.44 / % possible all: 61.6

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RL0

4rl0


Resolution: 2→42.212 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.25
RfactorNum. reflection% reflection
Rfree0.2285 2019 2.02 %
Rwork0.1858 --
obs0.1867 100028 90 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→42.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13584 0 227 1911 15722

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