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- PDB-6mgx: Crystal Structure of the New Deli Metallo Beta Lactamase Variant ... -

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Basic information

Entry
Database: PDB / ID: 6mgx
TitleCrystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella pneumoniae
ComponentsMetallo-beta-lactamase
KeywordsHYDROLASE / metallo beta lactamase / carbapenemases / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the New Deli Metallo Beta Lactamase Variant 6 Klebsiella pneumoniae
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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.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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,17311
Polymers51,4922
Non-polymers6819
Water81145
1
A: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0385
Polymers25,7461
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1346
Polymers25,7461
Non-polymers3885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-293 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.715, 73.901, 78.068
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 Metallo-beta-lactamase / NDM carbapenemase


Mass: 25745.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaNDM-6 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: G9JVE6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Sodium Citrate, 20% (w/v) PEG 4000, 20% (v/v) 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12723 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 618 / CC1/2: 0.731 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementStarting model: 4HL2

4hl2


Resolution: 2.6→39.034 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 617 4.86 %random
Rwork0.2094 ---
obs0.2118 12706 96.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→39.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 21 45 3448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053469
X-RAY DIFFRACTIONf_angle_d0.9874724
X-RAY DIFFRACTIONf_dihedral_angle_d17.3111199
X-RAY DIFFRACTIONf_chiral_restr0.055529
X-RAY DIFFRACTIONf_plane_restr0.002621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5996-2.86110.33811470.28512943X-RAY DIFFRACTION96
2.8611-3.27490.28981620.24353019X-RAY DIFFRACTION99
3.2749-4.12530.26521520.20233050X-RAY DIFFRACTION98
4.1253-39.03840.21871560.17543077X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0915-1.234-0.16782.2863-0.05863.5082-0.2119-0.1139-0.0853-0.0359-0.1521-0.15690.24530.61810.26630.34910.0221-0.09710.30510.01990.4876-14.4505-9.2627-5.1089
21.8462-0.39580.21731.3541-0.24921.10260.0441-0.0459-0.39690.1632-0.02510.22370.2893-0.0456-0.12870.3007-0.0088-0.03210.3014-0.01010.337-23.8998-5.9395-6.3962
31.55240.55030.80311.2715-0.00851.0150.0970.0922-0.00430.0762-0.054-0.1264-0.06260.0409-0.06560.28110.00220.00630.2769-0.01960.326-15.73749.1093-5.0123
42.38571.00661.16682.16581.01272.30850.13030.34350.1845-0.29440.0191-0.3394-0.25480.31710.02420.4940.02350.0550.3348-0.02160.3947-19.891751.1645-21.9918
58.0312-2.44173.15740.7688-0.93131.3249-0.05080.32540.28130.5074-0.1872-0.0798-0.15760.61670.11210.5172-0.0491-0.06150.4650.06290.3516-12.830845.5124-18.1972
60.72660.0474-0.37550.9296-0.15731.228-0.0528-0.0611-0.09430.06060.0134-0.09370.02440.0480.03790.27540.0027-0.01570.28420.00420.2874-20.739635.0235-14.1546
70.49150.1287-0.26281.65360.04691.1520.1101-0.0968-0.0895-0.16290.01120.19420.0432-0.1144-0.1540.27190.0176-0.02310.30450.00430.2858-16.770529.162-29.4508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 269 )
4X-RAY DIFFRACTION4chain 'B' and (resid 41 through 57 )
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 72 )
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 228 )
7X-RAY DIFFRACTION7chain 'B' and (resid 229 through 269 )

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