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- PDB-7k8l: Beta-lactamase, Unmixed -

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Basic information

Entry
Database: PDB / ID: 7k8l
TitleBeta-lactamase, Unmixed
ComponentsBeta-lactamase
KeywordsSTRUCTURAL PROTEIN / Beta-lactamase
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
PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.80001009193 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 ...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)113,9838
Polymers113,6034
Non-polymers3804
Water2,324129
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)28,4962
Polymers28,4011
Non-polymers951
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)28,4962
Polymers28,4011
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.910, 99.540, 112.580
Angle α, β, γ (deg.)90.000, 108.430, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
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
11ARGARGPHEPHE(chain 'A' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))AA65 - 7239 - 46
12ALAALAPROPRO(chain 'A' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))AA74 - 14348 - 117
13GLYGLYSERSER(chain 'A' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))AA146 - 265120 - 239
24ARGARGPHEPHE(chain 'B' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))BB65 - 7239 - 46
25ALAALAPROPRO(chain 'B' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))BB74 - 14348 - 117
26GLYGLYSERSER(chain 'B' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))BB146 - 265120 - 239
37ARGARGPHEPHE(chain 'C' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))CC65 - 7239 - 46
38ALAALAPROPRO(chain 'C' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))CC74 - 14348 - 117
39GLYGLYSERSER(chain 'C' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))CC146 - 265120 - 239
410ARGARGPHEPHE(chain 'D' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))DD65 - 7239 - 46
411ALAALAPROPRO(chain 'D' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))DD74 - 14348 - 117
412GLYGLYSERSER(chain 'D' and (resid 65 through 72 or resid 74 through 144 or resid 146 through 265))DD146 - 265120 - 239

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.79 Å3/Da / Density % sol: 67.51 %
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 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 41870 / % possible obs: 100 % / Redundancy: 754 % / CC1/2: 0.97 / Net I/σ(I): 5.64
Reflection shellResolution: 2.8→2.86 Å / Num. unique obs: 1600 / CC1/2: 0.23

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B5X

6b5x


Resolution: 2.80001009193→24.885 Å / SU ML: 0.469880827689 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.4695420974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.270239063808 1855 5.04021302032 %
Rwork0.204864659252 34949 -
obs0.208246917348 36804 87.9384497754 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1606878456 Å2
Refinement stepCycle: LAST / Resolution: 2.80001009193→24.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 20 129 8101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008591346858278124
X-RAY DIFFRACTIONf_angle_d1.0902719202511092
X-RAY DIFFRACTIONf_chiral_restr0.05614087463221276
X-RAY DIFFRACTIONf_plane_restr0.007205801011411468
X-RAY DIFFRACTIONf_dihedral_angle_d11.13134576734844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.87560.463631706396720.392524476361531X-RAY DIFFRACTION49.8445273632
2.8756-2.96010.420477071265980.3780475227231719X-RAY DIFFRACTION57.0845114672
2.9601-3.05550.395653858805960.353568661282039X-RAY DIFFRACTION66.1605206074
3.0555-3.16450.4091805051331320.3257741721422452X-RAY DIFFRACTION81.3858267717
3.1645-3.29090.3559140432011550.275423788952924X-RAY DIFFRACTION96.0386774797
3.2909-3.44030.320718883831800.2413790289232991X-RAY DIFFRACTION98.9700374532
3.4403-3.62120.2802195870391500.2069782137113050X-RAY DIFFRACTION99.7506234414
3.6212-3.84730.2863590017091640.1919083286043053X-RAY DIFFRACTION99.1982732038
3.8473-4.14310.2300631729081910.1685531047342986X-RAY DIFFRACTION98.8795518207
4.1431-4.55770.2037563603491610.1552144131833021X-RAY DIFFRACTION99.1586163914
4.5577-5.2120.2119341240611520.1436031758733034X-RAY DIFFRACTION99.1596638655
5.212-6.54670.219467751081560.1758261139433063X-RAY DIFFRACTION98.8636363636
6.5467-24.880.2159328235731480.1640214764933086X-RAY DIFFRACTION98.0594299576

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