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- PDB-6twt: Crystal structure of N-terminally truncated NDM-1 metallo-beta-la... -

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Basic information

Entry
Database: PDB / ID: 6twt
TitleCrystal structure of N-terminally truncated NDM-1 metallo-beta-lactamase
ComponentsMetallo beta lactamase NDM-1
KeywordsHYDROLASE / METALLO-BETA-LACTAMASE / NDM-1 / antibiotic resistance
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding / metal 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 / NDM-1
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsImiolczyk, B. / Czyrko-Horczak, J. / Brzezinski, K. / Jaskolski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Center for Research and Development (Poland)DesInMBL Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Flexible loops of New Delhi metallo-beta-lactamase modulate its activity towards different substrates.
Authors: Raczynska, J.E. / Imiolczyk, B. / Komorowska, M. / Sliwiak, J. / Czyrko-Horczak, J. / Brzezinski, K. / Jaskolski, M.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo beta lactamase NDM-1
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,22016
Polymers51,3782
Non-polymers84214
Water10,341574
1
A: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9717
Polymers25,6891
Non-polymers2826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2499
Polymers25,6891
Non-polymers5608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.482, 73.980, 77.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo beta lactamase NDM-1 / Metallo beta-lactamase / Metallo-beta-lactamase / NDM-1 / NDM carbapenemase / NDM-1 metallo-beta- ...Metallo beta-lactamase / Metallo-beta-lactamase / NDM-1 / NDM carbapenemase / NDM-1 metallo-beta-lactamase / NDM1 metallo-beta-lactamase / New Delhi Metallo carbapenemase-1 / New Delhi metallo-beta-lactamse 1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 25688.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaNDM-1, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, BANRA_05884, C3483_29595, C7V41_28630, D647_p47098, EC13450_007, FAQ72_26810, FAQ97_27095, FAS39_27275, NCTC13443_00040, ...Gene: blaNDM-1, bla NDM-1, blaNDM-1_1, blaNDM-1_2, blaNDM-1_3, blaNDM1, NDM-1, BANRA_05884, C3483_29595, C7V41_28630, D647_p47098, EC13450_007, FAQ72_26810, FAQ97_27095, FAS39_27275, NCTC13443_00040, p2146_00143, pCRE380_21, PMK1_ndm00067, PMK1_ndm00076, PMK1_ndm00085, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3531848_05178, TR3_031, TR4_031
Production host: Escherichia coli (E. coli) / References: UniProt: E9NWK5, UniProt: C7C422*PLUS

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Non-polymers , 5 types, 588 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MgCl2, CaCl2, imidazole, MES, MPD, PEG 1000, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8266 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 0.95→53.58 Å / Num. obs: 253359 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / CC1/2: 1 / Rrim(I) all: 0.064 / Net I/σ(I): 19.33
Reflection shellResolution: 0.95→1.01 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 40251 / CC1/2: 0.605 / Rrim(I) all: 1.592 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZR9

3zr9


Resolution: 0.95→53.58 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.447 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0141 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.015 / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1199 1014 0.4 %RANDOM
Rwork0.1046 ---
obs0.1047 252356 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 53.84 Å2 / Biso mean: 13.159 Å2 / Biso min: 5.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å2-0 Å2
2---0.89 Å20 Å2
3---0.18 Å2
Refinement stepCycle: final / Resolution: 0.95→53.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 30 622 4015
Biso mean--18.06 25.79 -
Num. residues----452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193744
X-RAY DIFFRACTIONr_bond_other_d0.0020.023390
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9345141
X-RAY DIFFRACTIONr_angle_other_deg0.94637882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67224.601163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62115574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4581519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214412
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02759
X-RAY DIFFRACTIONr_rigid_bond_restr5.43437134
X-RAY DIFFRACTIONr_sphericity_free20.8115428
X-RAY DIFFRACTIONr_sphericity_bonded7.38457238
LS refinement shellResolution: 0.951→0.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 73 -
Rwork0.278 18118 -
all-18191 -
obs--97.49 %

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