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- PDB-6ogo: Crystal structure of NDM-9 metallo-beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6ogo
TitleCrystal structure of NDM-9 metallo-beta-lactamase
ComponentsSUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9
KeywordsHYDROLASE / metallo-beta-lactamase / NDM
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsRaczynska, J.E. / Imiolczyk, B. / Jaskolski, M.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentreAMR/1/2015 Poland
National Center for Research and Development (Poland) 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
DepositionApr 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9
B: SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9
C: SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,22133
Polymers77,0673
Non-polymers2,15430
Water14,016778
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A: SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,50812
Polymers25,6891
Non-polymers81911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,28110
Polymers25,6891
Non-polymers5929
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,43211
Polymers25,6891
Non-polymers74310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.929, 122.929, 38.501
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein SUBCLASS B1 METALLO-BETA-LACTAMASE NDM-9


Mass: 25688.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: BK248_28090, BK292_25365, BK373_25580, BK383_27845, CA593_27010
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M2CSI6

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Non-polymers , 8 types, 808 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2M NaCl, 0.1M Phosphate/citrate pH 4.2, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.72931 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72931 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.398
11K, H, -L20.01
11-h,-k,l30.5
11-K, -H, -L40.091
ReflectionResolution: 1.43→61.46 Å / Num. obs: 120161 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.088 / Net I/σ(I): 16.5
Reflection shellResolution: 1.43→1.52 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 19202 / CC1/2: 0.71 / Rrim(I) all: 0.782 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q6x

3q6x
PDB Unreleased entry


Resolution: 1.43→61.46 Å / Cor.coef. Fo:Fc: 0.992 / Cor.coef. Fo:Fc free: 0.983 / SU B: 1.009 / SU ML: 0.019 / Cross valid method: FREE R-VALUE / ESU R: 0.007 / ESU R Free: 0.008 / Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.11632 3004 2.5 %RANDOM
Rwork0.07351 ---
obs0.07461 117209 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.072 Å2
Baniso -1Baniso -2Baniso -3
1--3.26 Å2-0 Å2-0 Å2
2---3.26 Å2-0 Å2
3---6.52 Å2
Refinement stepCycle: 1 / Resolution: 1.43→61.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5081 0 99 778 5958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0135395
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174921
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.6337335
X-RAY DIFFRACTIONr_angle_other_deg1.5861.57411414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0865713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64723.2250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55715801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6071523
X-RAY DIFFRACTIONr_chiral_restr0.1020.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021089
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7661.712769
X-RAY DIFFRACTIONr_mcbond_other5.7531.7082768
X-RAY DIFFRACTIONr_mcangle_it5.362.5593464
X-RAY DIFFRACTIONr_mcangle_other5.362.5613465
X-RAY DIFFRACTIONr_scbond_it11.3362.1592626
X-RAY DIFFRACTIONr_scbond_other11.3342.1592627
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1732.9583856
X-RAY DIFFRACTIONr_long_range_B_refined7.90622.3325989
X-RAY DIFFRACTIONr_long_range_B_other7.90522.3355990
X-RAY DIFFRACTIONr_rigid_bond_restr18.943310301
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.429→1.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 209 -
Rwork0.231 8473 -
obs--97.64 %

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