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- PDB-6b5y: Beta-lactamase, mixed with Ceftriaxone, 30ms time point, Shards c... -

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Basic information

Entry
Database: PDB / ID: 6b5y
TitleBeta-lactamase, mixed with Ceftriaxone, 30ms time point, Shards crystal form
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-Lactamase
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 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 2.75 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
DepositionSep 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)116,01210
Polymers113,6034
Non-polymers2,4086
Water2,576143
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0503
Polymers28,4011
Non-polymers6502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9552
Polymers28,4011
Non-polymers5551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0503
Polymers28,4011
Non-polymers6502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9552
Polymers28,4011
Non-polymers5551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.530, 96.030, 112.580
Angle α, β, γ (deg.)90.00, 109.68, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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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: 3.53 Å3/Da / Density % sol: 65.2 %
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: 2.75→19.34 Å / Num. obs: 38561 / % possible obs: 100 % / Redundancy: 526.16 % / CC1/2: 0.345 / Net I/σ(I): 6.4
Reflection shellResolution: 2.75→2.81 Å / Redundancy: 142 % / Mean I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementResolution: 2.75→19.34 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.61
RfactorNum. reflection% reflection
Rfree0.2506 1913 4.96 %
Rwork0.1931 --
obs0.1959 38561 94.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 154 143 8249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018272
X-RAY DIFFRACTIONf_angle_d1.72111308
X-RAY DIFFRACTIONf_dihedral_angle_d15.0954924
X-RAY DIFFRACTIONf_chiral_restr0.0641284
X-RAY DIFFRACTIONf_plane_restr0.0081504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.81860.34321230.28821974X-RAY DIFFRACTION72
2.8186-2.89450.4231890.29222264X-RAY DIFFRACTION82
2.8945-2.97940.36971280.26822438X-RAY DIFFRACTION88
2.9794-3.07520.34181370.24832606X-RAY DIFFRACTION94
3.0752-3.18470.30431360.22992708X-RAY DIFFRACTION97
3.1847-3.31160.27861550.21612700X-RAY DIFFRACTION98
3.3116-3.46150.24861730.19472686X-RAY DIFFRACTION98
3.4615-3.64280.26331190.18232731X-RAY DIFFRACTION97
3.6428-3.86940.24431260.18672674X-RAY DIFFRACTION96
3.8694-4.16540.22911440.18232726X-RAY DIFFRACTION98
4.1654-4.57950.22321470.16182738X-RAY DIFFRACTION99
4.5795-5.23070.20761500.16382781X-RAY DIFFRACTION100
5.2307-6.54740.24081540.19112791X-RAY DIFFRACTION99
6.5474-19.34740.21291320.17422831X-RAY DIFFRACTION99

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