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- PDB-4ram: Crystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M6... -

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Basic information

Entry
Database: PDB / ID: 4ram
TitleCrystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G
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
OPEN FORM - PENICILLIN G / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.495 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, G. / 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: Crystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, G. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility ...Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, G. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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.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_conn.ptnr2_label_seq_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)52,57313
Polymers51,3722
Non-polymers1,20211
Water6,666370
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2546
Polymers25,6861
Non-polymers5685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3197
Polymers25,6861
Non-polymers6336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-278 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.065, 79.212, 133.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25685.850 Da / Num. of mol.: 2 / Mutation: M67V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pMCSG50 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G / Benzylpenicillin


Mass: 336.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O4S / Comment: antibiotic*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.6 M sodium chloride, 0.1 M MES pH 6.5, 20 %(w/v) PEG-4000, 5 mM Penicillin G, 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: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 67683 / Num. obs: 67683 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 12.89 Å2 / Rsym value: 0.072 / Net I/σ(I): 47.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 4 / Num. unique all: 3327 / Rsym value: 0.738 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 4HL2

4hl2


Resolution: 1.495→37.966 Å / SU ML: 0.11 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.18 3391 5.05 %random
Rwork0.143 ---
all0.145 67087 --
obs0.145 67087 98.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.6 Å2
Refinement stepCycle: LAST / Resolution: 1.495→37.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 55 370 3977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063849
X-RAY DIFFRACTIONf_angle_d1.0715271
X-RAY DIFFRACTIONf_dihedral_angle_d14.8951366
X-RAY DIFFRACTIONf_chiral_restr0.043586
X-RAY DIFFRACTIONf_plane_restr0.005708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4952-1.51660.20531180.1522186230483
1.5166-1.53920.1821180.14422475259394
1.5392-1.56330.19771440.14362618276298
1.5633-1.58890.20741200.14222623274399
1.5889-1.61630.18471310.138726742805100
1.6163-1.64570.19161400.133626502790100
1.6457-1.67740.18081270.138726392766100
1.6774-1.71160.21440.140626592803100
1.7116-1.74880.20181320.137426522785100
1.7488-1.78950.21041570.126626692826100
1.7895-1.83430.15921490.127226562805100
1.8343-1.88390.16831550.123726712826100
1.8839-1.93930.15251350.124126572792100
1.9393-2.00190.1611730.124726112784100
2.0019-2.07340.17731730.133226652838100
2.0734-2.15640.17351510.134326722823100
2.1564-2.25460.1631450.13226642809100
2.2546-2.37340.17641530.140126782831100
2.3734-2.52210.16971460.146927032849100
2.5221-2.71680.18091410.153427042845100
2.7168-2.99010.18031320.156627412873100
2.9901-3.42250.18971330.152427432876100
3.4225-4.3110.15661320.137728092941100
4.311-37.9780.21331420.16762877301999

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