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- PDB-3srx: New Delhi Metallo-beta-Lactamase-1 Complexed with Cd -

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Basic information

Entry
Database: PDB / ID: 3srx
TitleNew Delhi Metallo-beta-Lactamase-1 Complexed with Cd
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta sandwich / 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 / 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
: / THIOCYANATE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
Title: New Delhi Metallo-beta-Lactamase-1 Complexed with Cd
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Binkowski, T.A. / Mire, J. / Sacchettini, J. / Joachimiak, A.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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)51,35116
Polymers50,2002
Non-polymers1,15114
Water2,090116
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6928
Polymers25,1001
Non-polymers5927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6588
Polymers25,1001
Non-polymers5587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.945, 108.945, 237.883
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-277-

HOH

21A-328-

HOH

31A-337-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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 37-270
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, 130 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 4.06 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Potassium thiocyanate, 20 % w/v Polyethylene glycol 3,350, 10 mM Cadmium Chloride, 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: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 28517 / Num. obs: 28517 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 44.27 Å2 / Rsym value: 0.103 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1292 / Rsym value: 0.741 / % possible all: 88.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: dev_761)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3Q6X

3q6x
PDB Unreleased entry


Resolution: 2.5→49.526 Å / SU ML: 0.66 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1999 7.54 %random
Rwork0.175 ---
all0.178 26525 --
obs0.178 26525 89.21 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.106 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 68.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.0501 Å20 Å2-0 Å2
2--8.0501 Å20 Å2
3----16.1003 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 31 116 3612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083599
X-RAY DIFFRACTIONf_angle_d1.2734901
X-RAY DIFFRACTIONf_dihedral_angle_d15.2051255
X-RAY DIFFRACTIONf_chiral_restr0.11541
X-RAY DIFFRACTIONf_plane_restr0.007650
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5001-2.56260.34591150.27841407152273
2.5626-2.63190.29041240.26141530165480
2.6319-2.70930.30041310.24361598172983
2.7093-2.79680.25741350.22871663179887
2.7968-2.89670.28341390.21521701184089
2.8967-3.01270.27491420.20141743188590
3.0127-3.14980.24631450.21321774191992
3.1498-3.31580.2431500.19331827197794
3.3158-3.52350.2231470.18071828197594
3.5235-3.79550.21421510.17491849200094
3.7955-4.17730.19281510.15791862201394
4.1773-4.78130.15221530.12531869202294
4.7813-6.02220.18891550.14321906206194
6.0222-49.53540.17681610.1611969213090
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)
10.2334-0.1218-0.04563.4830.8910.22290.38830.3896-0.0599-1.00010.08180.18330.0416-0.013-0.43851.2944-0.0628-0.07460.4372-0.00610.385844.8266-12.1852-4.4514
23.65651.84350.60525.13050.47341.79410.3083-0.05440.1005-0.5422-0.1667-0.3271-0.48710.2334-0.10351.2378-0.11530.00820.17360.01190.397953.0362-16.97910.4109
31.4558-0.92980.07682.0566-1.21782.6102-0.01610.19790.1545-0.91720.0188-0.2389-0.41980.2731-0.00240.7253-0.05880.0440.2634-0.02810.350456.935-21.14376.4707
41.51450.6293-0.27284.6005-0.05862.4139-0.0827-0.01360.0744-0.64540.13710.5311-0.6362-0.305-0.07550.5390.0616-0.11690.246-0.00610.35543.2378-19.488815.2977
52.01742.0081-4.24922.0115-4.85058.19890.0515-0.93370.4470.6206-0.03570.4263-0.2714-0.21270.04560.53350.083-0.11240.3595-0.00640.446337.7908-20.088720.5875
63.07930.77591.96621.90541.95954.9908-0.2773-0.76940.13830.55020.17150.13260.354-0.55550.06252.10870.6942-0.36621.18850.00880.50351.4295-3.652951.8202
71.7314-1.727-0.70936.64132.60753.0254-0.0035-0.4333-0.15610.84310.4024-0.02850.96410.2836-0.26251.48550.5444-0.51470.9291-0.29240.332951.70693.25445.8184
81.4957-2.8472-0.62529.50752.61782.0327-0.065-0.1031-0.07740.1937-0.0142-0.27760.42640.3512-0.12571.37770.7474-0.83520.8615-1.11351.049460.3118-1.146842.703
90.29310.29630.77810.36780.972.8202-0.2715-0.77510.65640.85720.9709-1.69590.26031.5154-0.53410.95970.3697-0.42191.2896-0.69031.182162.96772.685738.101
107.7779-4.0698-0.38578.93260.66115.8875-0.3173-0.58290.04240.63440.9769-1.09150.83940.8946-0.60540.71430.1293-0.14310.4295-0.20980.448354.3288-3.33431.3621
116.0681-0.422-0.30396.54743.17688.4478-0.0935-0.20040.6877-0.61750.26140.4019-1.009-0.384-0.18340.57260.1467-0.08330.3652-0.0940.39143.77425.644727.9443
122.0257-0.1167-1.78530.2012-1.19937.5474-0.7285-0.691-0.35211.44660.38140.67291.2915-0.14260.46450.87510.13880.07580.4228-0.04620.571444.3707-4.855936.7057
139.025-5.40191.829.2602-5.9095.9616-0.46690.60740.3398-1.3318-0.30441.2689-0.3721-0.99370.71390.87730.0211-0.26770.4215-0.16850.741137.43744.170527.1789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 34:70)
2X-RAY DIFFRACTION2chain 'A' and (resseq 71:94)
3X-RAY DIFFRACTION3chain 'A' and (resseq 95:212)
4X-RAY DIFFRACTION4chain 'A' and (resseq 213:255)
5X-RAY DIFFRACTION5chain 'A' and (resseq 256:270)
6X-RAY DIFFRACTION6chain 'B' and (resseq 42:57)
7X-RAY DIFFRACTION7chain 'B' and (resseq 58:82)
8X-RAY DIFFRACTION8chain 'B' and (resseq 83:94)
9X-RAY DIFFRACTION9chain 'B' and (resseq 95:170)
10X-RAY DIFFRACTION10chain 'B' and (resseq 171:212)
11X-RAY DIFFRACTION11chain 'B' and (resseq 213:239)
12X-RAY DIFFRACTION12chain 'B' and (resseq 240:256)
13X-RAY DIFFRACTION13chain 'B' and (resseq 257:270)

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