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- PDB-7mqn: Crystal structure of class C beta lactamase from Rhodobacter spha... -

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Basic information

Entry
Database: PDB / ID: 7mqn
TitleCrystal structure of class C beta lactamase from Rhodobacter sphaeroides
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase / AmpC / structural genomics / anti / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / peptidase activity / outer membrane-bounded periplasmic space / response to antibiotic / proteolysis
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsChang, C. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of class C beta lactamase from Rhodobacter sphaeroides
Authors: Chang, C. / Tesar, C. / Endres, M. / Joachimiak, A.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4448
Polymers75,8752
Non-polymers5706
Water6,954386
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2224
Polymers37,9371
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2224
Polymers37,9371
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.978, 72.090, 115.280
Angle α, β, γ (deg.)90.000, 132.790, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase


Mass: 37937.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: ampC, RSP_3749 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3IVS9, beta-lactamase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M Phosphate-citrate pH 4.2, 1.6M Sodium phosphate dibasic, 0.4M potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 49810 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.19 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.069 / Rrim(I) all: 0.138 / Χ2: 0.829 / Net I/σ(I): 7.1 / Num. measured all: 185389
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.80.66524720.7080.3880.7720.77299
2.24-2.283.80.52924640.6860.3130.6170.93499
2.28-2.323.80.51425020.8610.30.5970.75299.1
2.32-2.373.70.41924700.870.2460.4870.73799
2.37-2.423.80.36324700.8850.2110.4210.76998.4
2.42-2.483.80.32824930.8930.1910.3810.78798.6
2.48-2.543.70.30424440.9150.1780.3530.80599
2.54-2.613.70.25325070.9310.1490.2940.78699.4
2.61-2.693.70.22124910.9380.130.2580.83499.4
2.69-2.773.50.19624520.9410.1190.230.85997.7
2.77-2.873.50.17724610.9570.1070.2080.89797.6
2.87-2.993.90.14424860.9710.0820.1660.87799.4
2.99-3.123.80.13125060.9730.0740.1510.88699.5
3.12-3.293.80.11625180.9770.0660.1340.95299.5
3.29-3.493.80.10424870.980.0590.120.94599.3
3.49-3.763.70.09525230.9840.0540.110.89799.1
3.76-4.143.40.08924440.9720.0540.1040.83897.2
4.14-4.743.90.08425230.9830.0470.0960.73999.5
4.74-5.973.80.08325510.9830.0460.0950.62499.6
5.97-503.60.12325460.9580.0720.1430.91397.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SBC-Collectdata collection
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NJK

6njk


Resolution: 2.21→42.45 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 2261 4.94 %
Rwork0.182 43491 -
obs0.1839 45752 90.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.05 Å2 / Biso mean: 33.7265 Å2 / Biso min: 15.34 Å2
Refinement stepCycle: final / Resolution: 2.21→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5348 0 30 386 5764
Biso mean--37.53 34.67 -
Num. residues----702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.250.2858690.21121491156049
2.25-2.310.2584590.20891880193962
2.31-2.360.29231320.21562247237977
2.36-2.430.23031120.19692644275688
2.43-2.50.23771520.19992775292793
2.5-2.580.24551570.20982928308598
2.58-2.670.25211580.20332924308298
2.67-2.780.25651420.21562928307098
2.78-2.910.27981820.21612866304897
2.91-3.060.24561770.20922947312499
3.06-3.250.26671520.22977312999
3.25-3.50.20591510.18032994314599
3.5-3.850.20641430.15822970311398
3.85-4.410.1611420.14342950309297
4.41-5.550.17531220.14793026314899
5.55-42.450.20112110.18512944315596
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)
10.3731-0.1003-0.20480.41710.26030.3081-0.1905-0.703-0.02480.55940.2421-0.30720.53190.73570.38320.33410.1453-0.32930.46140.08880.2945-16.844733.696790.629
21.04020.2739-0.53030.78980.14871.3206-0.17430.0288-0.09890.09380.00190.06520.1667-0.0289-0.00120.20220.02130.00870.17430.01670.1872-34.027132.587873.6859
3-0.0089-0.0255-0.03430.02130.02770.0824-0.3058-0.1785-0.48070.28850.1738-0.14780.3375-0.01790.00030.55720.06730.18420.35330.11230.4531-24.615319.293566.0652
40.09060.02190.09260.02390.04570.183-0.0369-0.0833-0.16740.01710.0154-0.23960.14680.24040.00810.28230.10080.00840.3060.08170.3271-19.540128.278281.9664
50.9287-0.1668-0.70530.8406-0.0630.99430.11190.07020.11480.02420.0394-0.0639-0.0368-0.04590.00450.1574-0.0225-0.02920.1551-0.00430.1785-8.607338.186647.4983
60.3294-0.22890.04080.32640.15240.43470.0917-0.04320.0631-0.0085-0.0497-0.09610.00070.1292-00.2134-0.02590.01870.2273-0.02090.23771.891535.009345.0894
70.2560.1463-0.09660.2364-0.13850.13960.0643-0.01060.51770.21460.2085-0.0156-0.3825-0.15360.08170.31180.0120.04910.1967-0.07460.2884-9.365450.903755.7821
80.05970.01030.00510.02420.02-0.0081-0.08730.0010.37650.17440.2012-0.1717-0.4810.2750.00010.4607-0.05560.06370.29720.03680.5088-15.16352.645256.0384
90.2954-0.1662-0.02460.05740.0270.0650.0197-0.18930.14420.27660.0423-0.193-0.08280.1415-00.3074-0.04780.00730.2596-0.08360.2691.191843.614859.7821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 68 )A29 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 308 )A69 - 308
3X-RAY DIFFRACTION3chain 'A' and (resid 309 through 328 )A309 - 328
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 379 )A329 - 379
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 188 )B29 - 188
6X-RAY DIFFRACTION6chain 'B' and (resid 189 through 268 )B189 - 268
7X-RAY DIFFRACTION7chain 'B' and (resid 269 through 308 )B269 - 308
8X-RAY DIFFRACTION8chain 'B' and (resid 309 through 328 )B309 - 328
9X-RAY DIFFRACTION9chain 'B' and (resid 329 through 379 )B329 - 379

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