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- PDB-7k8e: Beta-lactamase mixed with Ceftriaxone, 5ms -

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Basic information

Entry
Database: PDB / ID: 7k8e
TitleBeta-lactamase mixed with Ceftriaxone, 5ms
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
Ceftriaxone / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.40005625978 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 26, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)115,09210
Polymers113,6034
Non-polymers1,4896
Water4,432246
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4962
Polymers28,4011
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4962
Polymers28,4011
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 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
Unit cell
Length a, b, c (Å)80.680, 98.780, 113.090
Angle α, β, γ (deg.)90.000, 108.600, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVAL(chain 'A' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))AA74 - 8048 - 54
12HISHISLEULEU(chain 'A' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))AA82 - 19256 - 166
13GLNGLNSERSER(chain 'A' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))AA194 - 265168 - 239
24ALAALAVALVAL(chain 'B' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))BB74 - 8048 - 54
25HISHISLEULEU(chain 'B' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))BB82 - 19256 - 166
26GLNGLNSERSER(chain 'B' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))BB194 - 265168 - 239
37ALAALAVALVAL(chain 'C' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))CC74 - 8048 - 54
38HISHISLEULEU(chain 'C' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))CC82 - 19256 - 166
39GLNGLNSERSER(chain 'C' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))CC194 - 265168 - 239
410ALAALAVALVAL(chain 'D' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))DD74 - 8048 - 54
411HISHISLEULEU(chain 'D' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))DD82 - 19256 - 166
412GLNGLNSERSER(chain 'D' and (resid 74 through 80 or resid 82 through 192 or resid 194 through 265))DD194 - 265168 - 239

NCS ensembles :
ID
1
2
3
4

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-9F2 / Ceftriaxone


Mass: 554.580 Da / Num. of mol.: 2 / 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.: 246 / 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: 3.76 Å3/Da / Density % sol: 67.28 %
Crystal growTemperature: 300 K / Method: microbatch / 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: 1.33 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 65232 / % possible obs: 100 % / Redundancy: 1758 % / CC1/2: 0.99 / Net I/σ(I): 6.67
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 1888 / CC1/2: 0.27

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
CrystFELdata scaling
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B5X

6b5x


Resolution: 2.40005625978→24.695 Å / SU ML: 0.39646216872 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.8299003843
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25040738568 2550 4.88852251596 %
Rwork0.234404553417 49613 -
obs0.235226856236 52163 79.2582125384 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.1175667829 Å2
Refinement stepCycle: LAST / Resolution: 2.40005625978→24.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 92 246 8290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003351027534028202
X-RAY DIFFRACTIONf_angle_d1.0694836371811206
X-RAY DIFFRACTIONf_chiral_restr0.04857096954141278
X-RAY DIFFRACTIONf_plane_restr0.004445909742721486
X-RAY DIFFRACTIONf_dihedral_angle_d12.96814132054884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.44620.45567284952900.4384829362261888X-RAY DIFFRACTION54.2363586509
2.4462-2.49610.488354171173870.4012659195871597X-RAY DIFFRACTION46.429556107
2.4961-2.55030.4062852364551220.3812188976562230X-RAY DIFFRACTION64.6509070918
2.5503-2.60950.435443404024880.3755575914981970X-RAY DIFFRACTION56.9925228469
2.6095-2.67470.3804462053641120.3568396440422359X-RAY DIFFRACTION67.4767886401
2.6747-2.7470.348432685727980.3647171636041999X-RAY DIFFRACTION57.736784141
2.747-2.82770.332973375804920.3594300925341974X-RAY DIFFRACTION56.4480874317
2.8277-2.91880.3879075154381120.3477167366782292X-RAY DIFFRACTION66.3904998619
2.9188-3.0230.3967964614421150.3290553837822622X-RAY DIFFRACTION75.5451283467
3.023-3.14380.3020707658731470.2971111032743087X-RAY DIFFRACTION88.0958866794
3.1438-3.28650.3025387320331820.2554565133533373X-RAY DIFFRACTION97.9878721058
3.2865-3.45940.274651876521990.2341846735123452X-RAY DIFFRACTION99.5094031071
3.4594-3.67540.2224179225071760.2074331249753483X-RAY DIFFRACTION99.7546346783
3.6754-3.95820.2206269253841890.1960815290333424X-RAY DIFFRACTION98.7698195735
3.9582-4.35450.1950117941182110.1838901908163423X-RAY DIFFRACTION99.235390497
4.3545-4.98020.1939613414651950.1727974419333448X-RAY DIFFRACTION99.3997271487
4.9802-6.25750.2051929423451560.2000345724623518X-RAY DIFFRACTION98.9762931034
6.2575-24.690.2033641851021790.2005386762993474X-RAY DIFFRACTION97.517351842

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