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- PDB-6xj3: Crystal structure of Class D beta-lactamase from Klebsiella quasi... -

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Basic information

Entry
Database: PDB / ID: 6xj3
TitleCrystal structure of Class D beta-lactamase from Klebsiella quasipneumoniae in complex with avibactam
ComponentsBeta-lactamase
KeywordsHYDROLASE / class D beta-lactamase / structural genomic / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae 700603 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChang, C. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Class D beta-lactamase from Klebsiella quasipneumoniae
Authors: Chang, C. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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_conn_type
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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,42016
Polymers118,7064
Non-polymers1,71412
Water8,773487
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0464
Polymers29,6771
Non-polymers3693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3647
Polymers29,6771
Non-polymers6886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0663
Polymers29,6771
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9442
Polymers29,6771
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.552, 88.669, 76.100
Angle α, β, γ (deg.)90.000, 99.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase


Mass: 29676.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae 700603 (bacteria)
Gene: oxa-2, blaOXA-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4LAV3, beta-lactamase

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Non-polymers , 6 types, 499 molecules

#2: Chemical
ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form


Mass: 267.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O6S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Calcium chloride, 0.1M Tris-chloride, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 75097 / % possible obs: 96.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.025 / Rrim(I) all: 0.046 / Χ2: 0.928 / Net I/σ(I): 12 / Num. measured all: 253183
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.882.30.32229970.8680.2650.420.95978.1
1.88-1.922.50.2932810.9060.2270.3710.94685
1.92-1.952.70.25535320.9220.1880.3190.91691.6
1.95-1.993.20.19337590.960.1280.2330.94797.1
1.99-2.043.60.16938190.9740.1050.20.98799.1
2.04-2.083.50.14738450.9780.0910.1731.00399.3
2.08-2.143.50.12438310.9830.0770.1470.99999.3
2.14-2.193.50.10338260.9880.0640.1221.02698.5
2.19-2.263.40.08838260.990.0560.1050.99698.9
2.26-2.333.30.08237970.990.0530.0970.97397.9
2.33-2.413.60.07138500.9930.0440.0830.93799.5
2.41-2.513.60.06538430.9940.040.0770.91999
2.51-2.633.50.05338470.9950.0330.0620.88598.9
2.63-2.763.50.04738250.9960.030.0560.87898.6
2.76-2.943.50.04438390.9950.0280.0520.87198.8
2.94-3.163.60.03938900.9960.0240.0450.80599.5
3.16-3.483.60.03438200.9970.0210.040.80598.5
3.48-3.993.50.03238340.9970.020.0380.84498.6
3.99-5.023.60.03439030.9960.0210.040.91299.4
5.02-503.50.03439330.9980.0220.0410.97798.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SBC-Collectdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K38

1k38


Resolution: 1.85→34.59 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 3605 4.95 %
Rwork0.1799 69209 -
obs0.1818 72814 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.4 Å2 / Biso mean: 24.1915 Å2 / Biso min: 2.42 Å2
Refinement stepCycle: final / Resolution: 1.85→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7928 0 107 487 8522
Biso mean--36.31 25.48 -
Num. residues----964
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.880.2745750.22141308138347
1.88-1.90.291850.23851627171258
1.9-1.930.28151110.23042069218073
1.93-1.960.27141560.2242421257787
1.96-1.990.27481620.20842684284695
1.99-2.020.24761270.19912801292899
2.02-2.050.25521460.19912839298599
2.05-2.090.28011480.19382773292199
2.09-2.130.20711340.19952825295999
2.13-2.180.22381460.19252810295699
2.18-2.220.24631510.18452766291799
2.22-2.270.23461350.19572790292599
2.27-2.330.26641390.1952796293598
2.33-2.390.23271520.19042826297899
2.39-2.470.26521490.2052793294299
2.47-2.540.21771390.19182834297399
2.54-2.640.22631420.18112802294499
2.64-2.740.24221680.18972762293099
2.74-2.870.25241340.19612815294998
2.87-3.020.21611620.19628302992100
3.02-3.210.25751410.18922815295699
3.21-3.450.23331290.17492839296899
3.45-3.80.16721440.16072795293998
3.8-4.350.15221610.140528533014100
4.35-5.480.1691390.13972824296398
5.48-34.590.18581300.1642912304299
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)
10.0005-0.0006-0.00010.0003-0.0002-0.00010.0009-0.01380.0062-0.0013-0.00250.0009-0.0072-0.0068-0.00080.16080.09040.05880.2482-0.04850.20926.544243.81313.2153
20.0033-0.0024-0.00270.00160.00070.00220.0182-0.0019-0.00740.0264-0.0214-0.0073-0.0043-0.0145-00.16960.02990.00130.25820.04250.178930.637234.94787.0755
30.02580.0224-0.03820.019-0.03270.05840.03670.0018-0.03140.0030.0540.01260.0197-0.06010.02170.12250.0236-0.07450.2896-0.06350.236229.942225.4892-6.4099
40.0027-0.0030.00240.01190.00610.02050.01180.0401-0.0264-0.0129-0.01370.00980.0018-0.0105-0.00940.22890.1104-0.10710.2707-0.10460.145545.618821.8383-19.345
50.00070.001-0.00010.0065-0.00130.00080.00850.0064-0.0185-0.01020.0026-0.00090.0144-0.013-0.00210.1779-0.0606-0.11930.3092-0.08690.304927.446316.7494-12.7573
60.013-0.0117-0.01510.03130.02750.02340.0402-0.0114-0.0907-0.0244-0.04260.0347-0.0206-0.1221-0.01370.0839-0.0082-0.01850.20540.02740.126638.270927.4835-1.4571
70.00270.00290.00140.0060.00080.00330.0272-0.00770.0234-0.0015-0.0158-0.0041-0.0083-0.00180.0010.14630.08390.04510.2623-0.00340.150336.65741.7366-3.5554
80.03280.0231-0.03030.0652-0.05740.0593-0.00880.02790.0261-0.0170.05380.0710.028-0.0690.08150.0274-0.0057-0.05660.03850.00040.100325.03440.082230.9921
90.002-0.0075-0.01040.03230.03040.0477-0.0267-0.0334-0.00980.0223-0.00490.0202-0.0078-0.0246-0.03710.14210.08420.0420.0738-0.01270.040736.346647.869254.5445
100.0051-0.00820.00830.0098-0.01090.0107-0.0307-0.00940.0614-0.0062-0.00920.0893-0.0818-0.0565-0.0890.05260.0623-0.0355-0.00150.01860.08329.782653.884838.4701
110.02140.03150.01390.05330.01720.0433-0.0212-0.0070.00020.0235-0.0220.07790.072-0.0713-0.05560.0315-0.05710.03860.0213-0.00080.067431.55835.195335.777
120.00470.00450.00250.03790.05220.0773-0.01770.00210.0460.01290.0658-0.0760.05340.12070.07930.06360.04710.01910.09670.03830.120166.592836.597744.3578
130.00230.0048-0.00440.0064-0.00560.00580.00870.03680.0096-0.0359-0.0201-0.03170.01760.01230.01670.15550.0210.11250.15440.13740.064356.096546.239520.3272
140.0015-0.0051-0.00570.09720.07240.0538-0.00470.04040.0453-0.06180.0122-0.1197-0.04840.08710.04750.0122-0.09710.02880.00220.09150.123364.016751.552336.3194
150.023-0.01330.00530.06130.00240.0355-0.01110.0311-0.0081-0.02750.0176-0.06890.08210.07020.02950.01620.1190.0405-0.07880.01850.057459.029833.353839.1278
160.07260.0431-0.00780.12660.09470.16150.08190.0254-0.04880.01170.0620.00780.02910.08740.1180.11450.0101-0.00780.1990.06030.099672.788127.91110.4369
170.0024-0.0026-0.00050.0029-0.00070.00120.0108-0.0098-0.00850.01920.0014-0.00260.0325-0.01680.01480.2123-0.0025-0.00070.34260.16610.185354.141621.845119.6549
180.0002-0.0004-0.00040.01180.00220.00070.0029-0.0461-0.06970.01820.01730.01440.06570.02570.02680.20460.0604-0.07680.10280.05790.218665.402814.44266.9111
190.027-0.0112-0.01940.02580.01850.01920.0614-0.03650.00690.0044-0.0027-0.0148-0.0210.04180.06090.1117-0.0212-0.03130.11190.03630.045565.245532.99872.5374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 38 )A25 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 56 )A39 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 85 )A57 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 133 )A86 - 133
5X-RAY DIFFRACTION5chain 'A' and (resid 134 through 167 )A134 - 167
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 241 )A168 - 241
7X-RAY DIFFRACTION7chain 'A' and (resid 242 through 265 )A242 - 265
8X-RAY DIFFRACTION8chain 'B' and (resid 24 through 85 )B24 - 85
9X-RAY DIFFRACTION9chain 'B' and (resid 86 through 132 )B86 - 132
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 196 )B133 - 196
11X-RAY DIFFRACTION11chain 'B' and (resid 197 through 266 )B197 - 266
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 84 )C24 - 84
13X-RAY DIFFRACTION13chain 'C' and (resid 85 through 132 )C85 - 132
14X-RAY DIFFRACTION14chain 'C' and (resid 133 through 196 )C133 - 196
15X-RAY DIFFRACTION15chain 'C' and (resid 197 through 265 )C197 - 265
16X-RAY DIFFRACTION16chain 'D' and (resid 25 through 84 )D25 - 84
17X-RAY DIFFRACTION17chain 'D' and (resid 85 through 133 )D85 - 133
18X-RAY DIFFRACTION18chain 'D' and (resid 134 through 196 )D134 - 196
19X-RAY DIFFRACTION19chain 'D' and (resid 197 through 265 )D197 - 265

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