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- PDB-6mh0: Crystal Structure of the New Deli Metallo Beta Lactamase Variant ... -

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Basic information

Entry
Database: PDB / ID: 6mh0
TitleCrystal Structure of the New Deli Metallo Beta Lactamase Variant 3 from Klebsiella pneumoniae
ComponentsMetallo-beta-lactamase NDM-3
KeywordsHYDROLASE / metallo beta lactamase / Carbapenemases / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


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 NDM-3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, G. / 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 3 from Klebsiella pneumoniae
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, G. / 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 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_ptnr1_label_alt_id / _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.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: Metallo-beta-lactamase NDM-3
B: Metallo-beta-lactamase NDM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,17116
Polymers51,4342
Non-polymers73714
Water5,242291
1
A: Metallo-beta-lactamase NDM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0868
Polymers25,7171
Non-polymers3697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase NDM-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0868
Polymers25,7171
Non-polymers3697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.185, 78.699, 130.790
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-3 / NDM-3 metallo-beta-lactamase


Mass: 25716.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NDM-3, blaNDM-3 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: I3VKD5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1.96 Å3/Da / Density % sol: 37.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.2 M Na/K phosphate pH6.2, 2.5 M NaCl

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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: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.65→37.537 Å / Num. obs: 49437 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 19.39 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2 / Num. unique obs: 2262 / CC1/2: 0.743 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→37.537 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.91
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2509 5.08 %random
Rwork0.1676 ---
obs0.1694 49365 98.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.1 Å2
Refinement stepCycle: LAST / Resolution: 1.65→37.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 22 291 3759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053540
X-RAY DIFFRACTIONf_angle_d0.754821
X-RAY DIFFRACTIONf_dihedral_angle_d4.5532450
X-RAY DIFFRACTIONf_chiral_restr0.055540
X-RAY DIFFRACTIONf_plane_restr0.005636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6454-1.6770.27661150.24771984X-RAY DIFFRACTION77
1.677-1.71120.27541350.22982576X-RAY DIFFRACTION99
1.7112-1.74840.26431280.20842587X-RAY DIFFRACTION100
1.7484-1.78910.23951320.18752634X-RAY DIFFRACTION100
1.7891-1.83390.21771300.17632569X-RAY DIFFRACTION100
1.8339-1.88340.23851540.1712612X-RAY DIFFRACTION100
1.8834-1.93890.23831630.16542569X-RAY DIFFRACTION100
1.9389-2.00140.21991310.17052622X-RAY DIFFRACTION100
2.0014-2.0730.191530.16722620X-RAY DIFFRACTION100
2.073-2.15590.22881450.16462599X-RAY DIFFRACTION100
2.1559-2.25410.19631310.1562657X-RAY DIFFRACTION100
2.2541-2.37290.18831280.16442622X-RAY DIFFRACTION100
2.3729-2.52150.23241490.17022638X-RAY DIFFRACTION100
2.5215-2.71620.21761340.17582653X-RAY DIFFRACTION100
2.7162-2.98940.18531560.18112649X-RAY DIFFRACTION100
2.9894-3.42170.21941410.16912686X-RAY DIFFRACTION100
3.4217-4.310.18471270.14612731X-RAY DIFFRACTION100
4.31-37.54630.17311570.15942848X-RAY DIFFRACTION100
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)
16.1477-0.8675-1.5344.12250.52196.3553-0.003-0.59840.95360.5128-0.0153-0.2782-0.85760.54470.04320.3021-0.0673-0.03250.2132-0.0640.430623.709425.815414.8305
22.30290.19120.04632.0538-0.88121.8750.0012-0.22570.40530.17620.02840.1428-0.1799-0.066-0.02910.14140.02630.01140.1219-0.03240.238913.900317.886913.4851
34.232-1.5845-0.54513.3428-0.43920.930.0082-0.01910.03560.12990.00950.201-0.0772-0.0370.00960.1227-0.0103-0.01960.11960.00720.115110.5561.323911.3157
42.28850.62570.27132.0914-0.70813.01930.0075-0.17720.11070.0826-0.0283-0.0746-0.0129-0.02860.02490.10930.01740.00730.128-0.01180.148222.56043.989114.9744
52.73480.7551-0.22633.95070.0261.83850.1226-0.1912-0.01890.2378-0.1195-0.2394-0.09660.06560.00260.1026-0.005-0.02170.15320.01230.145531.04454.430518.097
63.61512.99974.00625.27242.47287.70690.5876-0.8381-0.16060.92380.01550.42361.0642-0.5214-0.61470.59910.0148-0.0130.38120.03220.40649.6121-40.361624.8776
74.82130.50370.95234.22741.03274.6271-0.0076-0.2117-0.26550.4377-0.0894-0.11620.20810.07660.00960.2366-0.0283-0.00140.13740.03950.15438.2224-33.509619.1724
82.12050.21570.35932.93060.54883.4260.03610.034-0.15350.0467-0.0971-0.03050.23620.05420.05960.16840.0122-0.01440.12880.00870.122311.0701-32.100410.1579
91.6256-0.2278-0.47841.49720.1081.0354-0.00610.0253-0.0699-0.0166-0.0154-0.05090.0614-0.03860.01840.1568-0.0114-0.01530.15530.00180.137811.4335-17.458612.4067
101.99110.994-0.70124.3015-0.45142.44710.131-0.3378-0.01570.5494-0.1664-0.0459-0.0208-0.03930.00990.205-0.01030.00710.2390.0210.14812.6362-16.141426.7675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 228 )
5X-RAY DIFFRACTION5chain 'A' and (resid 229 through 269 )
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 48 )
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 72 )
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 118 )
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 212 )
10X-RAY DIFFRACTION10chain 'B' and (resid 213 through 269 )

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