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- PDB-7k8f: Beta-lactamase mixed with Ceftriaxone, 10ms -

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Basic information

Entry
Database: PDB / ID: 7k8f
TitleBeta-lactamase mixed with Ceftriaxone, 10ms
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.60003135588 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
Water4,522251
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)80.410, 98.160, 115.160
Angle α, β, γ (deg.)90.000, 109.760, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-9F2 / Ceftriaxone


Mass: 554.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N8O7S3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 3.78 Å3/Da / Density % sol: 67.48 %
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: 1.33 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: 2.6→24.9 Å / Num. obs: 51595 / % possible obs: 100 % / Redundancy: 966 % / CC1/2: 0.99 / Net I/σ(I): 6.34
Reflection shellResolution: 2.6→2.65 Å / Num. unique obs: 2045 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B5X

6b5x


Resolution: 2.60003135588→24.890545259 Å / SU ML: 0.397429958166 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.2772251046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.26442851635 2124 4.90825900079 %
Rwork0.217143948652 41150 -
obs0.219445342651 43274 83.3570905729 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.891003496 Å2
Refinement stepCycle: LAST / Resolution: 2.60003135588→24.890545259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 92 251 8295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00302809997898202
X-RAY DIFFRACTIONf_angle_d1.0253812698411206
X-RAY DIFFRACTIONf_chiral_restr0.04577440892131278
X-RAY DIFFRACTIONf_plane_restr0.003684470914171486
X-RAY DIFFRACTIONf_dihedral_angle_d12.65532518874884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.66040.386810867442730.3612856062111937X-RAY DIFFRACTION58.4302325581
2.6604-2.72690.479187882524950.3611752908492022X-RAY DIFFRACTION61.5944137329
2.7269-2.80050.413589061734900.3637816814311805X-RAY DIFFRACTION54.8798146539
2.8005-2.88280.3614283712971080.3603909674581822X-RAY DIFFRACTION56.0069645966
2.9757-3.08190.3946000228251450.3091902884932407X-RAY DIFFRACTION74.4240303295
3.0819-3.2050.3182823130251330.2767524166062962X-RAY DIFFRACTION89.9709302326
3.205-3.35060.2875490974891830.2521361666933191X-RAY DIFFRACTION97.5990743419
3.3506-3.52680.2482770276621980.2219365276663252X-RAY DIFFRACTION99.6821727824
3.5268-3.7470.2410843007731750.1927014069893238X-RAY DIFFRACTION99.6205487449
3.747-4.03520.2308065341241700.1846357773533274X-RAY DIFFRACTION99.5088124819
4.0352-4.43930.2407800980251480.1674808455133307X-RAY DIFFRACTION99.253088193
4.4393-5.07690.2185609982721590.1626910624263295X-RAY DIFFRACTION99.2814027019
5.0769-6.37850.239191590751770.1865555308833272X-RAY DIFFRACTION99.0238300316
6.3785-24.890.218114126071630.1873420505853273X-RAY DIFFRACTION96.5982569581

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