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- PDB-5jqj: Directed evolutionary changes in MBL super family - NDM-1 Round 1... -

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Basic information

Entry
Database: PDB / ID: 5jqj
TitleDirected evolutionary changes in MBL super family - NDM-1 Round 10 crystal-1
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / Phosphatase / Directed evolution / MBL super family / NDM-1
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; 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 speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsHong, N.-S. / Jackson, C.J. / Carr, P.D.
CitationJournal: To Be Published
Title: Enzyme evolvability is contingent on the initial sequence background
Authors: Baier, F. / Hong, N.-S. / Yang, G. / Carr, P.D. / Jackson, C. / Tokuriki, N.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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 type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5587
Polymers25,9881
Non-polymers5706
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.795, 137.724, 77.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-582-

HOH

31A-614-

HOH

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 25988.375 Da / Num. of mol.: 1 / Fragment: UNP residues 29-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1.94 Å3/Da / Density % sol: 36.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.75 / Details: 0.1 M MES pH 6.75, 1.3 M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.67→34.45 Å / Num. obs: 23318 / % possible obs: 97.22 % / Redundancy: 2 % / Biso Wilson estimate: 19.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02929 / Net I/σ(I): 17.93
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.89 / Num. measured obs: 1837 / % possible all: 77.72

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SPU

3spu


Resolution: 1.67→34.45 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.973 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18687 1195 5.1 %RANDOM
Rwork0.14436 ---
obs0.14659 22123 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.277 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0 Å2
2---0.22 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.67→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 28 266 1993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191835
X-RAY DIFFRACTIONr_bond_other_d0.0010.021734
X-RAY DIFFRACTIONr_angle_refined_deg2.0751.9472499
X-RAY DIFFRACTIONr_angle_other_deg0.9843.0013986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50223.76677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46915274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2791511
X-RAY DIFFRACTIONr_chiral_restr0.1380.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
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_it2.3272.036946
X-RAY DIFFRACTIONr_mcbond_other2.3232.033945
X-RAY DIFFRACTIONr_mcangle_it3.4633.0361193
X-RAY DIFFRACTIONr_mcangle_other3.4623.0391194
X-RAY DIFFRACTIONr_scbond_it2.932.392889
X-RAY DIFFRACTIONr_scbond_other2.932.392889
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1753.461306
X-RAY DIFFRACTIONr_long_range_B_refined7.45318.6722235
X-RAY DIFFRACTIONr_long_range_B_other7.45518.6562234
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 77 -
Rwork0.257 1256 -
obs--75.74 %

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