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- PDB-6b6a: Beta-Lactamase, 2secs timepoint, mixed, shards crystal form -

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Basic information

Entry
Database: PDB / ID: 6b6a
TitleBeta-Lactamase, 2secs timepoint, mixed, shards crystal form
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / Beta-Lactamase / ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


: / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ceftriaxone / Chem-FZS / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 2.298 Å
AuthorsPandey, S. / Schmidt, M.
CitationJournal: BMC Biol. / Year: 2018
Title: Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography.
Authors: Olmos, J.L. / Pandey, S. / Martin-Garcia, J.M. / Calvey, G. / Katz, A. / Knoska, J. / Kupitz, C. / Hunter, M.S. / Liang, M. / Oberthuer, D. / Yefanov, O. / Wiedorn, M. / Heyman, M. / Holl, M. ...Authors: Olmos, J.L. / Pandey, S. / Martin-Garcia, J.M. / Calvey, G. / Katz, A. / Knoska, J. / Kupitz, C. / Hunter, M.S. / Liang, M. / Oberthuer, D. / Yefanov, O. / Wiedorn, M. / Heyman, M. / Holl, M. / Pande, K. / Barty, A. / Miller, M.D. / Stern, S. / Roy-Chowdhury, S. / Coe, J. / Nagaratnam, N. / Zook, J. / Verburgt, J. / Norwood, T. / Poudyal, I. / Xu, D. / Koglin, J. / Seaberg, M.H. / Zhao, Y. / Bajt, S. / Grant, T. / Mariani, V. / Nelson, G. / Subramanian, G. / Bae, E. / Fromme, R. / Fung, R. / Schwander, P. / Frank, M. / White, T.A. / Weierstall, U. / Zatsepin, N. / Spence, J. / Fromme, P. / Chapman, H.N. / Pollack, L. / Tremblay, L. / Ourmazd, A. / Phillips, G.N. / Schmidt, M.
History
DepositionOct 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Oct 23, 2024Group: 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

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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)116,81112
Polymers113,6034
Non-polymers3,2078
Water7,566420
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.850, 95.310, 111.870
Angle α, β, γ (deg.)90.00, 109.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase / Ambler class A beta-lactamase


Mass: 28400.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: blaC, blaA, Rv2068c, MTCY49.07c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKD3, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-9F2 / Ceftriaxone


Mass: 554.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18N8O7S3 / Comment: antibiotic*YM
#4: Chemical ChemComp-FZS / (2R)-2-[(1S)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}-2-hydroxyethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / Ceftriaxone open, bound form


Mass: 399.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17N5O5S2 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 300 K / Method: microbatch / Details: Ammonium phosphate

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 65076 / % possible obs: 100 % / Redundancy: 329.82 % / Net I/σ(I): 5.4
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 59 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.354 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementResolution: 2.298→43.412 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 3200 4.92 %
Rwork0.2408 --
obs0.2421 65075 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.298→43.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 206 420 8578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098328
X-RAY DIFFRACTIONf_angle_d1.70911382
X-RAY DIFFRACTIONf_dihedral_angle_d15.0324950
X-RAY DIFFRACTIONf_chiral_restr0.061288
X-RAY DIFFRACTIONf_plane_restr0.0071516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2982-2.33250.34631080.34232141X-RAY DIFFRACTION75
2.3325-2.36890.38061290.32532377X-RAY DIFFRACTION84
2.3689-2.40780.34141270.31382438X-RAY DIFFRACTION87
2.4078-2.44930.33571260.29752555X-RAY DIFFRACTION90
2.4493-2.49380.35241270.29062587X-RAY DIFFRACTION92
2.4938-2.54180.35661350.27522605X-RAY DIFFRACTION92
2.5418-2.59370.30531190.26622640X-RAY DIFFRACTION93
2.5937-2.65010.31281480.26332610X-RAY DIFFRACTION94
2.6501-2.71170.31661370.25312677X-RAY DIFFRACTION94
2.7117-2.77950.28621440.24552685X-RAY DIFFRACTION95
2.7795-2.85460.2681400.25882691X-RAY DIFFRACTION96
2.8546-2.93860.30431370.25282721X-RAY DIFFRACTION96
2.9386-3.03340.31331320.24362764X-RAY DIFFRACTION97
3.0334-3.14180.2331160.23942812X-RAY DIFFRACTION98
3.1418-3.26760.31941320.2392817X-RAY DIFFRACTION99
3.2676-3.41620.24391580.23042830X-RAY DIFFRACTION100
3.4162-3.59630.23231820.20962776X-RAY DIFFRACTION100
3.5963-3.82150.23651740.22322807X-RAY DIFFRACTION100
3.8215-4.11630.24891380.21412858X-RAY DIFFRACTION100
4.1163-4.53020.23491480.21162839X-RAY DIFFRACTION100
4.5302-5.18470.24991380.22182846X-RAY DIFFRACTION100
5.1847-6.52870.27491540.24532879X-RAY DIFFRACTION100
6.5287-43.41960.21211510.23222920X-RAY DIFFRACTION100

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