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- PDB-4rl2: Structural and mechanistic insights into NDM-1 catalyzed hydrolys... -

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Basic information

Entry
Database: PDB / ID: 4rl2
TitleStructural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / NDM-1 antibiotic hydrolysis
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 / 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 / Alpha Beta
Similarity search - Domain/homology
Chem-3S3 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.008 Å
AuthorsFeng, H. / Ding, J. / Zhu, D. / Liu, X. / Xu, X. / Zhang, Y. / Zang, S. / Wang, D.-C. / Liu, W.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Structural and Mechanistic Insights into NDM-1 Catalyzed Hydrolysis of Cephalosporins.
Authors: Feng, H. / Ding, J. / Zhu, D. / Liu, X. / Xu, X. / Zhang, Y. / Zang, S. / Wang, D.C. / Liu, W.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 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_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)53,0858
Polymers52,0912
Non-polymers9946
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.620, 77.570, 132.310
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: 26045.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-3S3 / (1R)-2-({(R)-carboxy[(2R,5S)-4-carboxy-5-methyl-5,6-dihydro-2H-1,3-thiazin-2-yl]methyl}amino)-2-oxo-1-phenylethanaminium


Mass: 366.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N3O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 1.9 Å3/Da / Density % sol: 35.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 28% (w/v) PEG3350, 0.1 M Bis-Tris, pH 5.8 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 18, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.008→38.785 Å / Num. all: 26996 / Num. obs: 26843 / % possible obs: 99.43 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.008→2.12 Å / % possible all: 92.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 2.008→38.785 Å / SU ML: 0.17 / σ(F): 1.38 / Phase error: 17.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 1345 5.02 %random
Rwork0.1462 ---
all0.1486 26996 --
obs0.1486 26772 97.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.008→38.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 54 438 4086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093728
X-RAY DIFFRACTIONf_angle_d1.1115076
X-RAY DIFFRACTIONf_dihedral_angle_d14.2941364
X-RAY DIFFRACTIONf_chiral_restr0.046566
X-RAY DIFFRACTIONf_plane_restr0.005674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.008-2.07980.2141120.16422388X-RAY DIFFRACTION93
2.0798-2.1630.23651240.15412402X-RAY DIFFRACTION93
2.163-2.26150.22881320.14582441X-RAY DIFFRACTION96
2.2615-2.38070.21241450.15042469X-RAY DIFFRACTION97
2.3807-2.52980.19121220.14632554X-RAY DIFFRACTION99
2.5298-2.72510.21791160.15442592X-RAY DIFFRACTION99
2.7251-2.99920.19361520.14872573X-RAY DIFFRACTION100
2.9992-3.4330.19931380.14032603X-RAY DIFFRACTION100
3.433-4.32430.15381530.12912638X-RAY DIFFRACTION100
4.3243-38.79220.1771510.1532767X-RAY DIFFRACTION100

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