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- PDB-4gyq: Crystal Structure of New Delhi Metallo-beta-Lactamase-1 D223A mut... -

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Basic information

Entry
Database: PDB / ID: 4gyq
TitleCrystal Structure of New Delhi Metallo-beta-Lactamase-1 D223A mutant from Klebsiella pneumoniae
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / 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 fold
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 / SYNCHROTRON / MIR / Resolution: 1.351 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Binkowski, T.A. / Mire, J. / Sacchettini, J. / Joachimiak, A. / MCSG / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published / Year: 2012
Title: Crystal Structure of New Delhi Metallo-beta-Lactamase-1 D223A mutant from Klebsiella pneumoniae
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Binkowski, T.A. / Mire, J. / Sacchettini, J. / Joachimiak, A.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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)102,9068
Polymers102,6964
Non-polymers2114
Water18,8981049
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7983
Polymers25,6741
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7362
Polymers25,6741
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6982
Polymers25,6741
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase NDM-1


Theoretical massNumber of molelcules
Total (without water)25,6741
Polymers25,6741
Non-polymers00
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)51,5345
Polymers51,3482
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-2 kcal/mol
Surface area19100 Å2
MethodPISA
6
C: Beta-lactamase NDM-1
D: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3723
Polymers51,3482
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-13 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.140, 74.225, 76.599
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25673.904 Da / Num. of mol.: 4 / Mutation: D223A
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris pH 6.5, 25 %(w/v) PEG 3350, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2011 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 162811 / Num. obs: 162811 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 14.23 Å2 / Rsym value: 0.061 / Net I/σ(I): 9.3
Reflection shellResolution: 1.35→1.36 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique all: 5774 / Rsym value: 0.582 / % possible all: 69.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MIR
Starting model: PDB entry 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.351→34.036 Å / SU ML: 0.19 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1805 8178 5.02 %random, 5%
Rwork0.143 ---
all0.145 162771 --
obs0.145 162771 96.21 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.39 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.1296 Å20 Å2-1.4325 Å2
2---1.3972 Å2-0 Å2
3---1.5268 Å2
Refinement stepCycle: LAST / Resolution: 1.351→34.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 0 13 1049 7999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077420
X-RAY DIFFRACTIONf_angle_d1.14710130
X-RAY DIFFRACTIONf_dihedral_angle_d12.5622615
X-RAY DIFFRACTIONf_chiral_restr0.081117
X-RAY DIFFRACTIONf_plane_restr0.0061359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.351-1.36630.35641700.29683356352663
1.3663-1.38240.30792310.27963865409673
1.3824-1.39930.30942490.24924239448880
1.3993-1.4170.28572870.22324550483786
1.417-1.43560.24322310.20954882511391
1.4356-1.45530.27172760.19585082535895
1.4553-1.47610.24032980.18265234553298
1.4761-1.49810.21962450.155953275572100
1.4981-1.52150.21032730.139953475620100
1.5215-1.54650.17882780.137153855663100
1.5465-1.57310.20222650.132453565621100
1.5731-1.60170.18092760.134153245600100
1.6017-1.63250.20582570.117153835640100
1.6325-1.66590.16692770.110353855662100
1.6659-1.70210.1642720.10853005572100
1.7021-1.74170.16682830.1153845667100
1.7417-1.78520.16662530.118153485601100
1.7852-1.83350.16912810.124353425623100
1.8335-1.88740.19072960.122553235619100
1.8874-1.94840.17362770.124653915668100
1.9484-2.0180.16242830.130353685651100
2.018-2.09880.17462600.135553635623100
2.0988-2.19430.17712920.136253615653100
2.1943-2.30990.15753010.132953765677100
2.3099-2.45460.17022560.139453725628100
2.4546-2.64410.1763070.138153765683100
2.6441-2.910.16733050.146753375642100
2.91-3.33080.19343150.151153815696100
3.3308-4.19530.15193060.138653715677100
4.1953-34.04640.18052780.15835485576399

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