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- PDB-7rl8: Crystal Structure of C79A Mutant of Class D beta-lactamase from C... -

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Basic information

Entry
Database: PDB / ID: 7rl8
TitleCrystal Structure of C79A 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 activity / beta-lactamase / 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/transpeptidase-like
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 C79A 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 23, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)117,4147
Polymers117,1164
Non-polymers2983
Water12,556697
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,2791
Polymers29,2791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3852
Polymers29,2791
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3752
Polymers29,2791
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3752
Polymers29,2791
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.118, 93.878, 138.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-lactamase


Mass: 29279.025 Da / Num. of mol.: 4 / Mutation: C79A
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: pCPD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Magic / References: UniProt: Q188Q3, beta-lactamase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 7.2 mg/ml, 0.01M Tris pH 8.3, 5mM DDT; Screen: PACT (D4), 0.1M MMT buffer pH 7.0, 25% (w/v) PEG 1500

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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: 1.95→30 Å / Num. obs: 82125 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Rsym value: 0.074 / Χ2: 1.008 / Net I/σ(I): 25.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4066 / CC1/2: 0.844 / CC star: 0.957 / Rpim(I) all: 0.283 / Rrim(I) all: 0.776 / Rsym value: 0.722 / Χ2: 0.992 / % 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: 1.95→29.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.68 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 3989 4.9 %RANDOM
Rwork0.1778 ---
obs0.1793 78063 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.75 Å2 / Biso mean: 39.825 Å2 / Biso min: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.85 Å2
Refinement stepCycle: final / Resolution: 1.95→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8130 0 17 730 8877
Biso mean--72.54 40.07 -
Num. residues----1005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138415
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187694
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.63911335
X-RAY DIFFRACTIONr_angle_other_deg0.3391.5918007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.13451027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.79524.966437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.136151582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0161522
X-RAY DIFFRACTIONr_chiral_restr0.0610.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.029417
X-RAY DIFFRACTIONr_gen_planes_other0.0510.021685
LS refinement shellResolution: 1.951→2.002 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 287 -
Rwork0.236 5640 -
all-5927 -
obs--98.87 %
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)
11.59070.80120.26662.6399-0.39034.39240.08960.11040.0039-0.06680.0007-0.28460.03570.2792-0.09040.0130.0180.00730.0875-0.00360.0987.4943-19.8793-1.6749
21.3597-0.6847-0.17861.58490.18011.2924-0.0034-0.01590.24730.07460.01070.0145-0.0473-0.2361-0.00730.02440.0016-0.00520.1018-0.02450.081-18.7878-15.21930.276
30.4429-0.52060.0194.1024-3.3358.10960.0004-0.0693-0.00660.1094-0.15360.17160.1960.05020.15320.0375-0.0550.02290.1254-0.00760.0479-22.7375-27.39388.2688
41.5579-0.2650.40240.937-0.20362.1558-0.02510.02330.31370.0108-0.0427-0.1662-0.1097-0.01130.06780.02-0.003-0.00940.0416-0.01120.0926-6.0403-14.4841-1.45
52.84721.3215-1.58214.76-1.51893.30670.1851-0.18890.31550.4462-0.1105-0.2047-0.25810.1771-0.07460.0798-0.0193-0.0510.086-0.03470.1183.1918-14.9398.7517
69.17464.3662-0.17495.5334-0.17652.2309-0.02190.6426-0.2882-0.42730.1927-0.22090.24860.3115-0.17070.14220.09870.00620.1436-0.05980.13526.5022-45.9548-41.8273
71.3003-0.51240.22551.14610.16951.35590.03050.0022-0.04550.0638-0.0093-0.06980.03810.06-0.02120.05510.02060.0070.0170.00150.0688-4.8686-30.6131-28.6746
83.0707-0.3511-0.64363.736-0.27543.90060.11420.3752-0.3559-0.3293-0.10850.220.3253-0.181-0.00570.11830.0134-0.06840.0504-0.04920.153-12.9992-39.4222-38.6425
96.11423.14513.36525.41691.86073.28480.1680.3297-0.3217-0.2368-0.0029-0.34390.16490.3599-0.16510.07410.06-0.00140.0669-0.01130.0852.2029-36.4589-37.7424
103.18920.5461.90693.73920.7542.1806-0.00080.55870.0152-0.66960.0199-0.33060.06890.5474-0.01910.17330.07720.05810.18160.00840.12755.2846-38.3555-43.2865
112.6503-0.8380.01922.3176-0.49870.63850.18480.28110.2456-0.1232-0.06730.1773-0.0495-0.1438-0.11750.07370.08510.02970.11430.05730.0835-37.6942-9.4141-34.9227
122.9682-0.38990.11993.2221-1.05622.0790.181-0.04170.0769-0.1113-0.05520.17120.1255-0.1518-0.12580.1120.04020.06540.0650.01840.0874-43.6441-12.8743-25.2332
131.70080.1273-0.43133.0895-1.21422.64280.17760.12670.43610.05250.0061-0.1067-0.13950.2138-0.18360.15150.05140.08180.12140.03270.2345-28.4533-1.9153-33.1413
144.10582.32920.13382.8642-0.46922.33150.04150.56660.6072-0.29840.1290.4558-0.1632-0.2426-0.17050.14760.13260.02340.21070.15170.2205-43.52-1.6064-41.2305
151.1904-1.37680.13573.4495-4.21048.9096-0.0212-0.2612-0.14160.07940.10080.2089-0.07250.4345-0.07960.0819-0.00630.0380.13430.03240.0738-30.719915.8292-50.2054
162.5347-0.6986-0.256311.648-2.94713.31620.02340.36670.0097-0.4802-0.20160.78480.6429-0.79320.17820.2379-0.2640.02160.4099-0.11580.1884-14.497-66.4885-8.9907
171.88090.4078-0.20791.62320.75163.5847-0.0733-0.065-0.23340.3194-0.1255-0.18180.3168-0.29950.19880.2053-0.08390.01640.0555-0.02380.09693.623-53.29535.4938
180.6745-0.46940.26281.03111.48584.57650.00810.0296-0.06840.1519-0.23070.0760.5697-0.67260.22260.1314-0.13340.06630.1434-0.07140.0735-2.2562-56.6336-2.138
191.2163-0.9180.63123.7781-0.77027.1441-0.0490.1438-0.3307-0.1016-0.05890.21741.2183-0.84610.10790.3773-0.27830.10950.2158-0.10790.1234-4.8502-67.2961-7.4282
209.9137-4.1511-5.67113.94229.67497.68030.4806-0.53320.74860.0065-0.25540.1447-0.0689-0.0427-0.22520.1302-0.0994-0.03490.10940.00970.1498-5.8317-65.9775-28.6824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 71
2X-RAY DIFFRACTION2A72 - 161
3X-RAY DIFFRACTION3A162 - 172
4X-RAY DIFFRACTION4A173 - 262
5X-RAY DIFFRACTION5A263 - 288
6X-RAY DIFFRACTION6B41 - 60
7X-RAY DIFFRACTION7B61 - 194
8X-RAY DIFFRACTION8B195 - 223
9X-RAY DIFFRACTION9B224 - 254
10X-RAY DIFFRACTION10B255 - 288
11X-RAY DIFFRACTION11C41 - 140
12X-RAY DIFFRACTION12C141 - 192
13X-RAY DIFFRACTION13C193 - 223
14X-RAY DIFFRACTION14C224 - 287
15X-RAY DIFFRACTION15C288 - 294
16X-RAY DIFFRACTION16D41 - 70
17X-RAY DIFFRACTION17D71 - 169
18X-RAY DIFFRACTION18D170 - 239
19X-RAY DIFFRACTION19D240 - 286
20X-RAY DIFFRACTION20D287 - 294

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