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- PDB-4gyu: Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mut... -

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Basic information

Entry
Database: PDB / ID: 4gyu
TitleCrystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Protein Structure Initiative / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / alpha-beta-beta-alpha fold
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
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Binkowski, T.A. / Mire, J. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published / Year: 2012
Title: Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella pneumoniae
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Binkowski, T.A. / Mire, J. / Sacchettini, J. / Joachimiak, A.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5057
Polymers25,7941
Non-polymers7116
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.473, 101.473, 42.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase NDM-1 / NDM-1 / Metallo-beta-lactamase NDM-1


Mass: 25794.012 Da / Num. of mol.: 1 / Mutation: A121F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: C7C422, beta-lactamase

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Non-polymers , 5 types, 136 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Imidazole:HCl pH 8.0 1.0 M Sodium Citrate Tribasic, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2011 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 22017 / Num. obs: 22017 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 14.11 Å2 / Rsym value: 0.117 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 769 / Rsym value: 0.49 / % possible all: 65.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.803→43.939 Å / SU ML: 0.19 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1131 5.14 %random
Rwork0.152 ---
all0.154 21999 --
obs0.154 21999 94.12 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.927 Å2 / ksol: 0.438 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.5887 Å2-0 Å2-0 Å2
2--3.5887 Å20 Å2
3----7.1774 Å2
Refinement stepCycle: LAST / Resolution: 1.803→43.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 48 130 1974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011892
X-RAY DIFFRACTIONf_angle_d1.2352560
X-RAY DIFFRACTIONf_dihedral_angle_d14.386671
X-RAY DIFFRACTIONf_chiral_restr0.096280
X-RAY DIFFRACTIONf_plane_restr0.006337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8031-1.88510.2287970.17511850194768
1.8851-1.98450.20711330.14162349248285
1.9845-2.10880.17871380.135727632901100
2.1088-2.27170.16371490.135927502899100
2.2717-2.50030.18051720.142527472919100
2.5003-2.8620.20661530.151927622915100
2.862-3.60550.19531480.151327872935100
3.6055-43.95210.20671410.165428603001100
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)
10.8160.03990.28450.84680.81081.83330.21180.0993-0.2419-0.1453-0.1908-0.00090.0027-0.3934-0.0360.1665-0.0028-0.02030.23210.01040.156129.7838-38.566911.5073
21.1634-0.0675-0.13351.0670.00011.3151-0.04630.16860.0214-0.19830.0042-0.02790.10320.02430.04920.0836-0.001-0.00120.08260.00410.055516.4639-46.2345-0.4536
31.0971-0.2174-0.20441.02110.35131.799-0.0214-0.0580.00860.13230.0110.05150.0407-0.0382-0.03760.08830.016-00.09010.01010.06429.7492-42.79523.6693
42.4779-0.25621.56832.09670.20346.12350.00260.1019-0.16560.0130.1154-0.0040.11360.0061-0.04410.0846-0.00810.01780.06030.00840.088510.81-52.55425.9793
51.4656-0.45981.10180.6872-0.85241.29840.06540.0957-0.2071-0.0850.00330.12510.19190.0852-0.12070.0830.0043-0.00690.0929-0.00520.1155-0.4599-43.06370.1383
61.20910.69420.48582.260.43491.3736-0.0129-0.06790.13410.03120.04430.18270.1497-0.1513-0.04330.0140.01720.01370.0525-0.00170.1205-4.1189-33.37951.2799
71.6118-0.22820.03991.12080.52030.2487-0.1053-0.03490.04910.01730.05020.1058-0.0586-0.02060.04280.0697-0.0073-0.01290.1020.0090.12131.6552-30.48831.8277
81.87110.2775-0.65391.6015-1.0312.5762-0.051-0.03560.0749-0.02720.1491-0.1251-0.15540.172-0.14920.0844-0.0323-0.01350.1095-0.02820.114213.8869-31.4232-0.9046
91.5339-0.23620.26511.95320.89982.2087-0.08620.53320.135-0.3740.13620.025-0.0716-0.0621-0.00540.1689-0.0839-0.01050.2390.03760.13137.8515-27.0911-12.1461
102.2985-0.2167-0.07352.6077-0.33480.09660.01460.02970.1908-0.09890.1169-0.1929-0.00680.088-0.08640.0926-0.0294-0.00620.09060.0170.12116.7171-31.0787-0.8985
113.3005-0.31022.4681.2122-1.01865.1887-0.24290.82570.204-0.31850.31170.1354-0.16710.0995-0.00830.1588-0.09760.00980.22890.04070.152215.621-24.5921-12.3561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 29:43)
2X-RAY DIFFRACTION2chain 'A' and (resseq 44:70)
3X-RAY DIFFRACTION3chain 'A' and (resseq 71:94)
4X-RAY DIFFRACTION4chain 'A' and (resseq 95:108)
5X-RAY DIFFRACTION5chain 'A' and (resseq 109:152)
6X-RAY DIFFRACTION6chain 'A' and (resseq 153:170)
7X-RAY DIFFRACTION7chain 'A' and (resseq 171:194)
8X-RAY DIFFRACTION8chain 'A' and (resseq 195:215)
9X-RAY DIFFRACTION9chain 'A' and (resseq 216:239)
10X-RAY DIFFRACTION10chain 'A' and (resseq 240:255)
11X-RAY DIFFRACTION11chain 'A' and (resseq 256:269)

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