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- PDB-4rm5: Structural and mechanistic insights into NDM-1 catalyzed hydrolys... -

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Basic information

Entry
Database: PDB / ID: 4rm5
TitleStructural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / hydrolysis of beta-lactam antibiotics
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
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 19, 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
C: Beta-lactamase NDM-1
D: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04712
Polymers102,5234
Non-polymers5238
Water10,593588
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7623
Polymers25,6311
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7623
Polymers25,6311
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7623
Polymers25,6311
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7623
Polymers25,6311
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Beta-lactamase NDM-1
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5236
Polymers51,2622
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-166 kcal/mol
Surface area17040 Å2
MethodPISA
6
C: Beta-lactamase NDM-1
hetero molecules

D: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5236
Polymers51,2622
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2440 Å2
ΔGint-164 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.100, 68.120, 68.910
Angle α, β, γ (deg.)87.62, 88.34, 77.42
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 25630.836 Da / Num. of mol.: 4 / Mutation: D124N
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.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27% (w/v) PEG3350, 0.1 M Tris, pH 7.5, 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: Jun 21, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→35.015 Å / Num. all: 51417 / Num. obs: 51357 / % possible obs: 99.88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.21 Å / % possible all: 91.1

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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: 2.1→35.015 Å / SU ML: 0.16 / σ(F): 1.98 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 2277 5.06 %random
Rwork0.1589 ---
all0.1606 51417 --
obs0.1606 44974 94.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→35.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 8 588 7248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046800
X-RAY DIFFRACTIONf_angle_d0.8449259
X-RAY DIFFRACTIONf_dihedral_angle_d12.1972353
X-RAY DIFFRACTIONf_chiral_restr0.0331044
X-RAY DIFFRACTIONf_plane_restr0.0041219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14570.25441460.18392546X-RAY DIFFRACTION92
2.1457-2.19560.22631390.16582639X-RAY DIFFRACTION92
2.1956-2.25050.19551230.16432585X-RAY DIFFRACTION92
2.2505-2.31130.24221500.16782663X-RAY DIFFRACTION93
2.3113-2.37930.20491360.16792590X-RAY DIFFRACTION93
2.3793-2.45610.19131440.16772625X-RAY DIFFRACTION93
2.4561-2.54380.24761320.16982698X-RAY DIFFRACTION94
2.5438-2.64560.19421440.17122652X-RAY DIFFRACTION94
2.6456-2.7660.21011330.17092670X-RAY DIFFRACTION94
2.766-2.91180.19481470.1622718X-RAY DIFFRACTION95
2.9118-3.09410.21781600.17612688X-RAY DIFFRACTION95
3.0941-3.33280.20421310.16072705X-RAY DIFFRACTION96
3.3328-3.66790.1631380.14682719X-RAY DIFFRACTION96
3.6679-4.19790.16721750.13512725X-RAY DIFFRACTION97
4.1979-5.2860.13971350.13372766X-RAY DIFFRACTION97
5.286-35.02030.18611440.17142708X-RAY DIFFRACTION96

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