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- PDB-7k8k: Beta-lactamase mixed with Sulbactam, 60ms -

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Basic information

Entry
Database: PDB / ID: 7k8k
TitleBeta-lactamase mixed with Sulbactam, 60ms
ComponentsBeta-lactamase
KeywordsSTRUCTURAL PROTEIN / Beta-lactamase / Antibiotic / Hydrolase-antibiotic Complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
SULBACTAM / PHOSPHATE ION / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPandey, S. / Schmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Iucrj / Year: 2021
Title: Observation of substrate diffusion and ligand binding in enzyme crystals using high-repetition-rate mix-and-inject serial crystallography
Authors: Pandey, S. / Calvey, G. / Katz, A.M. / Malla, T.N. / Koua, F.H.M. / Martin-Garcia, J.M. / Poudyal, I. / Yang, J.H. / Vakili, M. / Yefanov, O. / Zielinski, K.A. / Bajt, S. / Awel, S. / ...Authors: Pandey, S. / Calvey, G. / Katz, A.M. / Malla, T.N. / Koua, F.H.M. / Martin-Garcia, J.M. / Poudyal, I. / Yang, J.H. / Vakili, M. / Yefanov, O. / Zielinski, K.A. / Bajt, S. / Awel, S. / Doerner, K. / Frank, M. / Gelisio, L. / Jernigan, R. / Kirkwood, H. / Kloos, M. / Koliyadu, J. / Mariani, V. / Miller, M.D. / Mills, G. / Nelson, G. / Olmos, J.L.J. / Sadri, A. / Sato, T. / Tolstikova, A. / Xu, W. / Ourmazd, A. / Spence, J.C.H. / Schwander, P. / Barty, A. / Chapman, H.N. / Fromme, P. / Mancuso, A.P. / Phillips, G.N.J. / Bean, R. / Pollack, L. / Schmidt, M.
History
DepositionSep 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)114,92012
Polymers113,6034
Non-polymers1,3178
Water3,567198
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7293
Polymers28,4011
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7313
Polymers28,4011
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7293
Polymers28,4011
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7313
Polymers28,4011
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.910, 99.530, 112.500
Angle α, β, γ (deg.)90.000, 108.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase


Mass: 28400.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: blaC, ERS027646_02769 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A655AHQ9, beta-lactamase
#2: Chemical ChemComp-0RN / SULBACTAM / (2S,5R)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid 4,4-dioxide


Mass: 233.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#4: Chemical ChemComp-TSL / TRANS-ENAMINE INTERMEDIATE OF SULBACTAM


Mass: 235.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
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: 3.78 Å3/Da / Density % sol: 67.46 %
Crystal growTemperature: 300 K / Method: batch mode / Details: Ammonium Phosphate

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Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.1 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→27.57 Å / Num. obs: 45344 / % possible obs: 100 % / Redundancy: 463 % / CC1/2: 0.97 / Net I/σ(I): 4.27
Reflection shellResolution: 2.7→2.72 Å / Num. unique obs: 1800 / CC1/2: 0.21

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B5X

6b5x


Resolution: 2.7→27.47 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.849 / SU B: 20.425 / SU ML: 0.369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.964 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2925 1890 4.9 %RANDOM
Rwork0.2148 ---
obs0.2187 36435 82.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 181.45 Å2 / Biso mean: 40.902 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.31 Å2
2---0.63 Å20 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 2.7→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 80 198 8230
Biso mean--105.75 27.6 -
Num. residues----1060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138186
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177580
X-RAY DIFFRACTIONr_angle_refined_deg1.671.65411188
X-RAY DIFFRACTIONr_angle_other_deg1.1921.57717458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.49651056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6520.642436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.458151214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2291576
X-RAY DIFFRACTIONr_chiral_restr0.0620.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021752
LS refinement shellResolution: 2.7→2.769 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 88 -
Rwork0.489 1401 -
all-1489 -
obs--43.91 %

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