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- PDB-3rkk: Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Kleb... -

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Basic information

Entry
Database: PDB / ID: 3rkk
TitleCrystal Structure of New Delhi Metallo-Beta-Lactamase-1 from Klebsiella pneumoniae
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta structure / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Binkowski, T.A. / Babnigg, G. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: Plos One / Year: 2011
Title: Structure of Apo- and Monometalated Forms of NDM-1 A Highly Potent Carbapenem-Hydrolyzing Metallo-beta-Lactamase
Authors: Kim, Y. / Tesar, C. / Mire, J. / Jedrzejczak, R. / Binkowski, A. / Babnigg, G. / Sacchettini, J. / Joachimiak, A.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Dec 20, 2017Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,38915
Polymers50,2002
Non-polymers1,18913
Water3,063170
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7578
Polymers25,1001
Non-polymers6577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6337
Polymers25,1001
Non-polymers5326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.760, 50.862, 70.717
Angle α, β, γ (deg.)90.00, 106.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25100.152 Da / Num. of mol.: 2 / Fragment: sequence database residues 39-270 / Mutation: Q36N, Q37Y
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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.17 M Ammonium sulfate 25.5 % (w/v) PEG 4000, 15 % (v/v) Glycerol, 5 mM zinc acetate, pH 7.5, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 16892 / Num. obs: 16892 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 24.97 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 5.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2 / Num. unique all: 709 / % possible all: 80.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→40.65 Å / SU ML: 0.32 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.283 842 5.03 %random
Rwork0.208 ---
all0.212 16745 --
obs0.212 16745 97.55 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.454 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.8486 Å2-0 Å210.8873 Å2
2---7.2363 Å2-0 Å2
3---8.0849 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 70 170 3609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173570
X-RAY DIFFRACTIONf_angle_d1.6154857
X-RAY DIFFRACTIONf_dihedral_angle_d16.8591235
X-RAY DIFFRACTIONf_chiral_restr0.125531
X-RAY DIFFRACTIONf_plane_restr0.011636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.35-2.49720.40551240.28992321244586
2.4972-2.690.31311370.22827042857100
2.69-2.96060.31661360.206126822818100
2.9606-3.38890.29761670.196526972864100
3.3889-4.26890.24161500.171527072857100
4.2689-40.65610.24861280.216727922920100
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)
10.0350.0209-0.02080.0248-0.04580.1780.0115-0.00620.03270.0432-0.00860.01-0.03050.07680.09610.0542-0.01230.04110.01170.0315-0.0524-0.27910.971628.4679
20.05870.01940.03150.25370.03830.023-0.04990.0865-0.03570.0440.0487-0.11840.01260.05730.00160.0747-0.01070.00520.0987-0.00750.08615.7136-3.204724.2806
30.02280.01280.0420.1764-0.03390.1573-0.05360.0468-0.0624-0.0298-0.0137-0.1611-0.01050.0704-0.04120.0797-0.01680.01120.0495-0.01680.1096-7.9402-10.121219.3427
40.08730.00050.08390.0647-0.04690.1144-0.03930.01630.01930.0078-0.0398-0.00840.0572-0.0043-0.08650.0868-0.0466-0.01110.03270.01760.158126.2428-37.69425.2085
50.0008-0.00710.00530.0654-0.05690.0798-0.0020.02070.0189-0.0188-0.0399-0.07020.02310.05730.00850.0759-0.02080.04980.1492-0.04170.166415.2215-33.67612.7654
60.27420.00390.00530.0128-0.0080.0038-0.00860.0082-0.058-0.01460.0557-0.06870.00770.01960.03270.0453-0.02940.0080.07740.01910.176522.8402-30.253810.0262
70.1180.08660.01830.06910.03750.08050.0123-0.0078-0.0414-0.00290.0416-0.02980.016-0.00960.14460.02870.00880.04550.04360.03050.130320.9999-34.012914.7987
80.05350.0232-0.04670.019-0.01180.0591-0.02020.0134-0.02380.02010.00030.0433-0.003-0.0362-0.06330.02040.00080.05670.05140.02210.092613.5566-20.828420.2463
90.01210.0108-0.03240.0383-0.05070.1012-0.00230.01260.01-0.04140.02040.01690.0297-0.04530.10270.11080.0329-0.08250.1303-0.08810.117620.8143-15.05715.3657
100.0180.00430.00920.0480.02230.0137-0.00610.0136-0.0249-0.01090.0147-0.06540.02170.005-0.00820.1986-0.07510.06380.0788-0.03760.132421.8664-19.02382.4605
110.0007-0.0079-0.00620.11060.0490.05430.0035-0.01160.00150.0335-0.01010.04240.0215-0.00690.02460.1322-0.0521-0.00790.1012-0.06650.123910.616-11.73272.903
120.08610.0044-0.06450.13060.10180.1340.0538-0.0307-0.0631-0.00270.0640.104-0.011-0.05250.08390.1225-0.0236-0.03190.10150.04350.09623.2447-19.9121-0.1922
130.13040.0390.07120.11910.04450.05950.01680.04380.00740.03210.0135-0.0031-0.0175-0.0191-0.00520.10250.03470.03360.11870.0320.155913.2971-9.961-4.1177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 44:118)
2X-RAY DIFFRACTION2chain 'A' and (resseq 119:215)
3X-RAY DIFFRACTION3chain 'A' and (resseq 216:270)
4X-RAY DIFFRACTION4chain 'B' and (resseq 45:57)
5X-RAY DIFFRACTION5chain 'B' and (resseq 58:70)
6X-RAY DIFFRACTION6chain 'B' and (resseq 71:94)
7X-RAY DIFFRACTION7chain 'B' and (resseq 95:137)
8X-RAY DIFFRACTION8chain 'B' and (resseq 138:166)
9X-RAY DIFFRACTION9chain 'B' and (resseq 167:194)
10X-RAY DIFFRACTION10chain 'B' and (resseq 195:215)
11X-RAY DIFFRACTION11chain 'B' and (resseq 216:239)
12X-RAY DIFFRACTION12chain 'B' and (resseq 240:255)
13X-RAY DIFFRACTION13chain 'B' and (resseq 256:270)

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