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- PDB-6ue2: 1.85 Angstrom Resolution Crystal Structure of Class D beta-lactam... -

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Basic information

Entry
Database: PDB / ID: 6ue2
Title1.85 Angstrom Resolution Crystal Structure 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 / TRIETHYLENE GLYCOL / PROPANOIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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: Microbiol Resour Announc / Year: 2023
Title: A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.
Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / ...Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / Minor, W. / Joachimiak, A. / Savchenko, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)118,6058
Polymers118,1824
Non-polymers4224
Water14,952830
1
A: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1833
Polymers59,0912
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4215
Polymers59,0912
Non-polymers3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.983, 93.200, 137.583
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: 29545.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium 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): magic / References: UniProt: Q188Q3, beta-lactamase

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Non-polymers , 5 types, 834 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 8.25 mg/ml, 0.01M Tris pH 8.3; Screen: PACT (C4), 0.1 M PCB 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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2019 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 93218 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Rsym value: 0.074 / Χ2: 1.164 / Net I/σ(I): 25.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4591 / CC1/2: 0.71 / Rpim(I) all: 0.353 / Rrim(I) all: 0.871 / Rsym value: 0.794 / Χ2: 0.999 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.56 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.525 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.12
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 4651 5 %RANDOM
Rwork0.165 ---
obs0.1666 88476 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.49 Å2 / Biso mean: 34.519 Å2 / Biso min: 9.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.85→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8153 0 28 881 9062
Biso mean--67.8 35.45 -
Num. residues----1007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187857
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.64411554
X-RAY DIFFRACTIONr_angle_other_deg0.3821.5918395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.53951052
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.44324.765447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.601151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1161525
X-RAY DIFFRACTIONr_chiral_restr0.0690.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.029636
X-RAY DIFFRACTIONr_gen_planes_other0.050.021731
LS refinement shellResolution: 1.852→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 316 -
Rwork0.261 6202 -
all-6518 -
obs--95.19 %
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)
11.28420.7679-0.25332.6201-0.4223.8360.02370.08930.048-0.1480.0153-0.2238-0.12440.2544-0.03910.02090.01070.030.11660.0250.11437.0359-19.7387-1.778
21.5541-0.4439-0.28261.53580.11230.8314-0.0024-0.03280.1996-0.0001-0.00740.0386-0.0629-0.11710.00990.03240.008-0.01830.0848-0.00510.0813-19.4865-15.45680.5979
31.4237-0.14360.39060.86240.09051.3452-0.01540.0380.2295-0.0152-0.0278-0.0785-0.1370.02820.04320.0226-0.00120.00590.03160.00960.0824-4.9481-14.82491.3683
42.421.50190.64466.2502-0.23041.73830.02010.204-0.1294-0.5418-0.0293-0.25930.30950.30870.00920.2010.11190.0220.0999-0.04370.17856.2608-47.4807-38.8039
51.4864-0.83440.36321.6816-0.16221.48550.09280.0358-0.1234-0.0016-0.0278-0.02210.09790.0109-0.06490.09320.00570.00450.0011-0.00050.0701-7.0884-30.771-30.6511
64.53421.47031.45863.82630.63792.37750.01160.452-0.1421-0.6342-0.0477-0.34250.06510.45810.03610.20730.09070.03610.12780.0030.1734.8394-37.8017-40.8847
73.2358-0.6849-0.47321.7607-0.25770.63760.19780.53760.3188-0.2177-0.05350.1122-0.092-0.2721-0.14430.09970.08030.01990.16590.08690.0638-37.5616-8.7194-34.9959
82.24410.5889-0.88411.0862-0.6241.33990.10840.25420.252-0.10820.03630.051-0.1011-0.1791-0.14470.09620.05390.0390.05140.04720.0722-37.1335-8.3667-29.2224
91.42452.1974-1.74373.6378-2.38773.0054-0.10580.52810.4619-0.31470.59250.5765-0.0831-0.7025-0.48670.32430.12020.00920.53830.3120.4511-42.52431.0613-41.9248
102.74111.6213-0.21282.78920.46732.6731-0.14260.0821-0.3720.2198-0.0491-0.21520.532-0.29160.19170.2286-0.0890.0680.0402-0.03390.157-0.4571-58.0142-0.949
111.0368-0.24350.0051.60530.85933.5669-0.0910.0125-0.12150.2918-0.1994-0.00690.4613-0.44670.29040.1385-0.09810.05030.0779-0.04130.081-3.3901-54.54551.7309
120.2789-0.24320.51690.53730.20424.54710.0270.0937-0.14530.1213-0.28530.11291.1016-0.550.25830.4086-0.21070.12180.2081-0.10610.2331-5.9136-66.7421-10.2702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 72
2X-RAY DIFFRACTION2A73 - 166
3X-RAY DIFFRACTION3A167 - 288
4X-RAY DIFFRACTION4B41 - 71
5X-RAY DIFFRACTION5B72 - 234
6X-RAY DIFFRACTION6B235 - 289
7X-RAY DIFFRACTION7C41 - 137
8X-RAY DIFFRACTION8C138 - 234
9X-RAY DIFFRACTION9C235 - 294
10X-RAY DIFFRACTION10D40 - 138
11X-RAY DIFFRACTION11D139 - 239
12X-RAY DIFFRACTION12D240 - 294

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