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- PDB-6wy4: Crystal Structure of Wild Type Class D beta-lactamase from Clostr... -

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Basic information

Entry
Database: PDB / ID: 6wy4
TitleCrystal Structure of Wild Type 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
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: 1.8 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 Wild Type 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
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id
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

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)117,3736
Polymers117,2444
Non-polymers1292
Water16,232901
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,3111
Polymers29,3111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4172
Polymers29,3111
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)29,3111
Polymers29,3111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3342
Polymers29,3111
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.332, 93.261, 138.053
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: 29311.088 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (strain 630) (bacteria)
Strain: 630 / Gene: CD630_04580 / Plasmid: pMCSG104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): (DE3)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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 7.6 mg/ml, 0.01M Tris pH 8.3, 5mM DDT; Screen: PEG's II (F8), 0.1 M Sodium acetate, 25% (w/v) PEG 4000, 8% (w/v) Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 24, 2019 / Details: BE
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 102923 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.076 / Rsym value: 0.07 / Χ2: 1.005 / Net I/σ(I): 24.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5107 / CC1/2: 0.756 / CC star: 0.928 / Rpim(I) all: 0.34 / Rrim(I) all: 0.864 / Rsym value: 0.793 / Χ2: 1 / % 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: 1.8→29.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.018 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 5203 5.1 %RANDOM
Rwork0.1762 ---
obs0.1779 97282 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.64 Å2 / Biso mean: 30.952 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0 Å2
2---0.56 Å20 Å2
3---0.67 Å2
Refinement stepCycle: final / Resolution: 1.8→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8127 0 8 968 9103
Biso mean--57.76 33.45 -
Num. residues----1004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138466
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187735
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.6411409
X-RAY DIFFRACTIONr_angle_other_deg0.3441.5918110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.14351037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.60524.91442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.785151596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7741523
X-RAY DIFFRACTIONr_chiral_restr0.0630.21083
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.029509
X-RAY DIFFRACTIONr_gen_planes_other0.0510.021704
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 389 -
Rwork0.247 7086 -
all-7475 -
obs--99.99 %
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)
11.34190.7262-0.14842.0251-0.76874.20340.03610.16130.0008-0.0885-0.0168-0.1688-0.12090.227-0.01920.01630.00970.01970.12270.0120.04147.0536-19.6225-1.7184
21.7176-0.62-0.46211.3880.41041.06450.04420.0350.2773-0.007-0.02230.0103-0.07-0.1113-0.02190.03920.00070.00390.09220.00610.0602-18.9183-14.51570.4669
33.54051.2957-1.09811.7438-0.56041.84430.1489-0.09830.01510.0573-0.09630.05070.0084-0.0828-0.05260.0309-0.0134-0.00380.0980.00220.0033-15.2773-24.58971.5655
41.8505-0.34860.48591.5302-0.46391.90740.02780.0820.32620.016-0.0465-0.0863-0.15090.07790.01870.0319-0.01170.02020.0490.00530.0661-4.372-12.98841.035
58.30490.6713-1.95733.89680.01477.33780.19-0.0720.6620.1766-0.0004-0.1651-0.34380.1434-0.18960.0512-0.04190.00590.05010.00160.10918.2686-9.91684.3294
61.59161.69830.17986.96540.45132.33510.11030.2216-0.2312-0.4634-0.0183-0.17760.29510.3211-0.0920.15030.10710.0130.1041-0.03630.15715.7294-48.1477-38.9945
71.8649-0.64140.35611.3074-0.30361.28570.0381-0.0366-0.02460.0633-0.0139-0.0599-0.01020.0511-0.02410.08520.00410.01340.0313-0.00630.029-5.8614-28.441-27.879
83.5118-0.0912-0.12542.556-0.30561.79460.12310.2878-0.3706-0.3184-0.09330.17820.2358-0.0102-0.02980.13950.03-0.05260.0322-0.05020.0883-9.9076-38.272-38.278
98.0516.07614.43236.25773.354.17760.11120.1928-0.4989-0.22480.0076-0.4430.1030.3315-0.11870.09970.0646-0.00110.0774-0.0190.12493.1214-38.1145-36.6166
104.01591.11681.25044.63440.17262.23820.01420.6067-0.204-0.7189-0.0226-0.34850.01030.54970.00840.2120.08470.0630.2102-0.02420.1185.3804-38.1201-43.0016
115.07832.01050.01674.4656-0.72542.65530.13250.43061.2620.10330.18610.6214-0.2967-0.4044-0.31860.17980.17580.12520.20680.23210.4923-46.43747.3607-36.3533
122.588-0.8717-1.05721.31630.23471.34460.12380.27380.0515-0.0546-0.05280.0842-0.0361-0.1918-0.07090.07070.02290.01310.08520.02970.0237-34.3216-15.7934-31.0522
134.0870.53162.92796.53964.77889.6338-0.0121-0.1611-0.6552-0.3851-0.0830.33870.149-0.22950.09510.1078-0.00140.00050.03840.00610.1538-47.5105-22.2131-27.6211
142.37930.8881-0.95841.7148-0.42681.98740.10920.51770.5434-0.11330.16730.1615-0.2003-0.3231-0.27650.12730.09260.05590.15510.13370.1403-39.0187-3.8782-35.365
152.45933.9168-4.43516.487-7.10798.013-0.05910.13940.37260.03230.68640.66480.0862-0.3064-0.62730.37670.1865-0.02140.86680.30420.4767-37.28658.2387-47.4114
162.84460.09520.32826.4864-0.66924.5075-0.05550.21280.0897-0.0656-0.24150.15010.5259-0.57310.2970.1405-0.16340.08380.2155-0.11390.1751-14.7988-65.8811-9.8695
173.38761.6596-0.37782.76770.59451.9060.062-0.139-0.44140.5731-0.1824-0.42580.2458-0.05410.12040.2034-0.0424-0.04440.01550.03170.12745.3053-54.81492.4762
181.13750.05830.3722.15961.2623.5353-0.00150.0044-0.12660.4012-0.2502-0.00190.2859-0.31250.25170.1379-0.07680.03240.0513-0.03020.0558-3.0718-53.58830.9768
190.9276-1.2061.59282.5009-1.9635.57560.0939-0.008-0.22460.0904-0.14420.14920.7847-0.4340.05030.2892-0.15950.08840.0984-0.05270.1775-5.6772-66.8576-2.9308
200.836-0.851-2.10361.82531.26747.7498-0.02830.13160.04310.1826-0.23050.10790.3839-0.38880.25870.2228-0.07930.08870.1283-0.07770.249-6.7663-67.9564-20.0881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 71
2X-RAY DIFFRACTION2A72 - 158
3X-RAY DIFFRACTION3A159 - 193
4X-RAY DIFFRACTION4A194 - 277
5X-RAY DIFFRACTION5A278 - 287
6X-RAY DIFFRACTION6B41 - 70
7X-RAY DIFFRACTION7B71 - 192
8X-RAY DIFFRACTION8B193 - 235
9X-RAY DIFFRACTION9B236 - 255
10X-RAY DIFFRACTION10B256 - 288
11X-RAY DIFFRACTION11C41 - 73
12X-RAY DIFFRACTION12C74 - 158
13X-RAY DIFFRACTION13C159 - 172
14X-RAY DIFFRACTION14C173 - 274
15X-RAY DIFFRACTION15C275 - 294
16X-RAY DIFFRACTION16D41 - 68
17X-RAY DIFFRACTION17D69 - 138
18X-RAY DIFFRACTION18D139 - 234
19X-RAY DIFFRACTION19D235 - 276
20X-RAY DIFFRACTION20D277 - 294

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