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- PDB-7rlr: Crystal Structure of K83A Mutant of Class D beta-lactamase from C... -

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Entry
Database: PDB / ID: 7rlr
TitleCrystal Structure of K83A Mutant of Class D beta-lactamase from Clostridium difficile 630
ComponentsBeta-lactamase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / blaD
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Rosas-Lemus, M. / Jedrzejczak, R. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of K83A Mutant of Class D beta-lactamase from Clostridium difficile 630
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Rosas-Lemus, M. / Jedrzejczak, R. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)117,45918
Polymers116,8404
Non-polymers61914
Water15,385854
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3404
Polymers29,2101
Non-polymers1303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4295
Polymers29,2101
Non-polymers2194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3043
Polymers29,2101
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3866
Polymers29,2101
Non-polymers1765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.534, 93.621, 138.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase


Mass: 29209.986 Da / Num. of mol.: 4 / Mutation: K83A
Source method: isolated from a genetically manipulated source
Details: Class D beta-lactamase / Source: (gene. exp.) Clostridioides difficile (bacteria) / Strain: 630 / Gene: CD630_04580 / Plasmid: pMCSG104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Magic / References: UniProt: Q188Q3, beta-lactamase

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Non-polymers , 5 types, 868 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.5 mg/ml, 0.01M Tris pH 8.3, 5mM DDT; Screen: PEGSs II (D1), 0.1M Sodium acetate, 0.1M HEPES pH 7.5, 22% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2020 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 90491 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Rsym value: 0.068 / Χ2: 1.008 / Net I/σ(I): 26.7
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4507 / CC1/2: 0.779 / CC star: 0.936 / Rpim(I) all: 0.321 / Rrim(I) all: 0.853 / Rsym value: 0.79 / Χ2: 1.006 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UE2

6ue2


Resolution: 1.88→29.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.55 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 4441 4.9 %RANDOM
Rwork0.1684 ---
obs0.1699 85969 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.67 Å2 / Biso mean: 33.134 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0 Å2
2---1.25 Å20 Å2
3---0.81 Å2
Refinement stepCycle: final / Resolution: 1.88→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8114 0 33 886 9033
Biso mean--39.75 36.73 -
Num. residues----1006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187758
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.6411397
X-RAY DIFFRACTIONr_angle_other_deg0.3451.5918149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.69851037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.76425.057437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.754151607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.711523
X-RAY DIFFRACTIONr_chiral_restr0.0620.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.029489
X-RAY DIFFRACTIONr_gen_planes_other0.0510.021696
LS refinement shellResolution: 1.881→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 317 -
Rwork0.228 6132 -
all-6449 -
obs--97.88 %
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)
11.19810.5563-0.2862.3877-0.40392.92140.07240.15740.0075-0.11210.0037-0.1605-0.11360.2635-0.07610.02010.0120.01920.1671-0.00210.05826.9632-19.8125-1.7635
21.1902-0.3402-0.36811.31250.2420.99140.06690.02430.17750.0104-0.0240.0299-0.096-0.1273-0.04290.03530.01040.00780.12440.00330.0325-19.5603-15.29510.3725
31.10710.2562-0.05761.7095-0.37721.32190.06460.02520.0483-0.0242-0.0252-0.0116-0.0033-0.0614-0.03950.02720.00570.00330.1207-0.00470.0045-12.879-20.679-2.2417
46.42630.67075.22632.34610.87847.5906-0.14160.26210.5904-0.10020.0339-0.2331-0.51120.21190.10770.0573-0.00970.03620.02760.02350.1254-7.9854-3.0121-2.9244
51.87450.5125-0.12833.3421-1.62942.48710.05540.03820.24850.0234-0.0564-0.0877-0.12640.12780.0010.0104-0.00030.00960.0805-0.01520.0482-2.3142-15.64792.3414
61.96140.6572-1.18752.8908-0.82462.15960.1255-0.11050.12240.2542-0.0281-0.1103-0.1350.1132-0.09740.056-0.011-0.03120.1154-0.02980.04862.1739-15.75628.8945
76.9893.8697-0.61536.5145-1.04392.2946-0.02380.3771-0.2399-0.68370.1192-0.15650.32220.2142-0.09550.18010.07920.04490.1149-0.03770.14776.2166-46.0563-41.3926
80.4376-0.14350.14835.64871.79062.39740.0343-0.0738-0.20860.0592-0.0184-0.26210.26740.1269-0.01590.10810.0803-0.01060.10620.01330.17666.1441-48.6371-32.5478
91.526-0.4870.23070.9787-0.14221.36490.0035-0.02320.02550.0287-0.0067-0.0113-0.0244-0.03670.00320.0480.01130.01780.0499-0.00870.0134-9.1638-26.9932-28.6305
101.7255-0.43520.08641.71650.25251.54990.07840.0816-0.1822-0.1509-0.06950.07780.110.0372-0.00890.06320.02950.00290.0273-0.01060.0301-5.7206-35.4399-33.3329
1111.27297.59617.40656.8574.48345.30950.13860.2341-0.4866-0.07240.0522-0.48030.21790.2659-0.19080.04990.05740.01130.0792-0.0170.09214.2379-36.7333-35.7174
123.85680.14731.19373.56970.36452.20120.09920.5076-0.1799-0.6213-0.0804-0.35010.05370.3991-0.01880.1610.07650.06950.1444-0.01420.07174.7208-38.6794-43.004
134.62391.5755-0.47174.043-0.53072.56980.12460.08040.78350.01260.02080.4149-0.1734-0.2877-0.14530.12380.10950.07470.12110.12090.3905-46.45317.0437-36.619
142.6079-0.8187-0.59031.54110.19520.7360.12490.3145-0.0092-0.1328-0.0780.11130.0359-0.1237-0.04690.07080.02950.00920.11780.02190.0243-33.35-17.3217-34.4992
152.4612-0.7812-0.0461.5697-0.59231.34280.12770.02980.1237-0.0309-0.0250.0906-0.022-0.1169-0.10270.05840.0220.05280.07120.02230.0596-42.8967-13.4154-25.1006
161.26990.6871-0.53682.738-1.40712.06380.08440.17580.3832-0.01070.0250.0227-0.19280.0956-0.10940.0830.03270.06510.08480.06190.1675-28.4896-1.5226-34.0851
173.71731.6244-0.28283.196-0.72932.12570.05150.51120.5603-0.35950.07260.3178-0.0562-0.2731-0.12410.09290.08260.03260.1720.14470.1697-44.0815-2.2796-41.0587
182.1323-1.53280.30482.6208-2.625212.25010.0147-0.1148-0.20990.09930.19830.35460.14660.3804-0.2130.05040.00470.03050.09420.04360.0704-30.64415.5328-49.7552
192.9957-0.30140.5357.4187-0.17143.4854-0.06080.090.08840.0869-0.23050.37480.4951-0.62740.29130.1022-0.12990.09020.1673-0.11490.166-15.1846-66.1606-8.6891
201.83050.7995-0.13281.94770.94691.9966-0.0562-0.1454-0.21740.4171-0.1428-0.14720.131-0.09920.19890.1978-0.038-0.02350.05820.0230.07713.3884-52.38354.3875
217.7416-2.9328-4.16312.171-1.17613.8274-0.2678-0.8307-0.4440.6282-0.0910.03390.20620.27560.35880.4234-0.0506-0.05050.19170.03710.07044.1092-60.854918.4735
221.02610.02950.4761.46570.50692.9296-0.04640.0224-0.07160.2404-0.22360.13370.2432-0.27060.270.0841-0.0620.05270.0591-0.04910.0484-3.2557-56.1898-3.061
230.69190.22250.33680.5755-0.28584.88960.0208-0.0129-0.23820.1812-0.20490.10770.7003-0.22630.18420.2626-0.11770.1290.1407-0.08430.2307-5.6147-66.9343-8.1505
245.2634-0.25820.880910.33964.25021.9381-0.1712-0.27260.40660.18880.07660.06880.0556-0.03570.09460.0842-0.00090.00940.06830.0180.0764-5.5001-66.3029-29.8603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 72
2X-RAY DIFFRACTION2A73 - 164
3X-RAY DIFFRACTION3A165 - 204
4X-RAY DIFFRACTION4A205 - 222
5X-RAY DIFFRACTION5A223 - 260
6X-RAY DIFFRACTION6A261 - 287
7X-RAY DIFFRACTION7B41 - 60
8X-RAY DIFFRACTION8B61 - 75
9X-RAY DIFFRACTION9B76 - 164
10X-RAY DIFFRACTION10B165 - 234
11X-RAY DIFFRACTION11B235 - 253
12X-RAY DIFFRACTION12B254 - 288
13X-RAY DIFFRACTION13C41 - 73
14X-RAY DIFFRACTION14C74 - 138
15X-RAY DIFFRACTION15C139 - 192
16X-RAY DIFFRACTION16C193 - 227
17X-RAY DIFFRACTION17C228 - 286
18X-RAY DIFFRACTION18C287 - 294
19X-RAY DIFFRACTION19D41 - 71
20X-RAY DIFFRACTION20D72 - 162
21X-RAY DIFFRACTION21D163 - 172
22X-RAY DIFFRACTION22D173 - 239
23X-RAY DIFFRACTION23D240 - 288
24X-RAY DIFFRACTION24D289 - 294

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