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- PDB-6d1a: Crystal structure of NDM-1 complexed with compound 1 -

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Basic information

Entry
Database: PDB / ID: 6d1a
TitleCrystal structure of NDM-1 complexed with compound 1
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE/HYDROLASE inhibitor / beta-lactamase / carbapenemase / phosphonate / inhibitor / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / Chem-TWB / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103158-04 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Authors: Pemberton, O.A. / Jaishankar, P. / Akhtar, A. / Adams, J.L. / Shaw, L.N. / Renslo, A.R. / Chen, Y.
History
DepositionApr 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 9, 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_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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 type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1206
Polymers24,6031
Non-polymers5175
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.780, 59.860, 42.020
Angle α, β, γ (deg.)90.000, 97.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 24602.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TWB / [(6,7-dimethyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid


Mass: 268.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 50 mM Potassium phosphate monobasic, 10 mM Calcium chloride, 25% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→27.92 Å / Num. obs: 56079 / % possible obs: 98.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 13.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.043 / Rrim(I) all: 0.084 / Rsym value: 0.072 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.25-1.323.70.94480560.3810.0240.0470.0497.4
3.95-27.923.80.0418480.9940.0220.0440.03899.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.18 Å27.92 Å
Translation5.18 Å27.92 Å

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Processing

Software
NameVersionClassification
iMOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.8.0phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZF

4tzf


Resolution: 1.25→27.92 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.5 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.181 5346 5.04 %
Rwork0.1471 --
obs0.1488 56067 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.77 Å2 / Biso mean: 22.7781 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.25→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 28 259 1989
Biso mean--25.24 37.66 -
Num. residues----229
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 (%)
1.25-1.26420.33211630.32493296345992
1.2642-1.27910.31561380.30713297343592
1.2791-1.29470.31321510.30153234338592
1.2947-1.31110.30622010.27863287348893
1.3111-1.32830.29281990.27083167336692
1.3283-1.34650.31132070.2583301350893
1.3465-1.36570.26181740.24293220339493
1.3657-1.38610.26681590.22923323348293
1.3861-1.40780.26481780.2173401357994
1.4078-1.43090.24361370.20833280341793
1.4309-1.45550.23681480.19193321346994
1.4555-1.4820.21211560.18683343349994
1.482-1.51050.212170.1773260347794
1.5105-1.54130.20611330.17173430356395
1.5413-1.57490.18721360.15883350348694
1.5749-1.61150.22652020.15453383358595
1.6115-1.65180.19411530.14443348350195
1.6518-1.69640.17031730.13933428360196
1.6964-1.74630.19282040.13253362356696
1.7463-1.80270.16111940.12863344353896
1.8027-1.86710.17562050.1313354355996
1.8671-1.94190.19531810.12963404358596
1.9419-2.03020.16162030.12663413361697
2.0302-2.13720.15351910.12433407359897
2.1372-2.27110.16352400.11983384362497
2.2711-2.44630.17441970.13193445364298
2.4463-2.69230.13641710.13373455362698
2.6923-3.08150.17141800.13443465364598
3.0815-3.88070.16611820.1223503368599
3.8807-27.93070.15161730.13293514368799

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