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- PDB-4hl2: New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed wit... -

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Basic information

Entry
Database: PDB / ID: 4hl2
TitleNew Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin
ComponentsBeta-lactamase NDM-1
KeywordsHydrolase/Antibiotic / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / alpha-beta-beta-alpha sandwich / hydrolase / Hydrolase-Antibiotic 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 / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ZZ7 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. / Sacchettini, J. / Joachimiak, A.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Aug 14, 2019Group: Data collection / Category: computing
Revision 1.3Sep 20, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase NDM-1
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,93216
Polymers51,4362
Non-polymers1,49614
Water11,025612
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4648
Polymers25,7181
Non-polymers7477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4688
Polymers25,7181
Non-polymers7507
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-36 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.190, 79.171, 134.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailstwo monomers in the asymmetric unit

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Components

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


Mass: 25717.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulphate, 0.1 M Bis-Tris pH 5.5, 25 %(w/v) PEG 3350, 100 mM ampicillin, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.5166 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2011 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.5166 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 185255 / Num. obs: 185255 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 7.76 Å2 / Rsym value: 0.089 / Net I/σ(I): 6.4
Reflection shellResolution: 1.05→1.06 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.871 / Num. unique all: 5746 / Rsym value: 0.023 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
SHELXrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.05→17.561 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 13.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.157 9286 5.03 %random
Rwork0.133 ---
all0.134 184744 --
obs0.134 184744 94.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.8 Å2
Refinement stepCycle: LAST / Resolution: 1.05→17.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 83 612 4304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174168
X-RAY DIFFRACTIONf_angle_d1.8085713
X-RAY DIFFRACTIONf_dihedral_angle_d13.8241527
X-RAY DIFFRACTIONf_chiral_restr0.121623
X-RAY DIFFRACTIONf_plane_restr0.011779
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.0503-1.06230.24962880.21065358564687
1.0623-1.07480.21512750.19185448572390
1.0748-1.08790.20352740.18175513578789
1.0879-1.10170.19463000.17055475577590
1.1017-1.11610.17873180.15695505582390
1.1161-1.13140.16092800.14995517579790
1.1314-1.14760.17123120.15075517582990
1.1476-1.16470.15912960.14715563585991
1.1647-1.18290.17432860.13885610589691
1.1829-1.20230.16922820.14215599588192
1.2023-1.2230.16972900.13635653594392
1.223-1.24530.16782950.1355718601393
1.2453-1.26920.16093320.13075713604593
1.2692-1.29510.15973120.12545765607794
1.2951-1.32330.14452920.12335806609894
1.3233-1.3540.14633170.12625872618995
1.354-1.38790.15073360.125876621296
1.3879-1.42540.14953420.11295896623696
1.4254-1.46730.13443240.10886021634598
1.4673-1.51460.1433200.11036030635098
1.5146-1.56880.13483280.10286091641998
1.5688-1.63150.12693010.10556158645999
1.6315-1.70570.13192960.10596169646599
1.7057-1.79560.12653220.11461906512100
1.7956-1.90790.13813280.118161586486100
1.9079-2.0550.14583520.117462556607100
2.055-2.26150.14033120.121262636575100
2.2615-2.58780.15553040.133263156619100
2.5878-3.2570.15963400.141763476687100
3.257-17.56370.18393320.15666057638992

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