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- PDB-7k8h: Beta-lactamase mixed with Ceftriaxone, 50ms -

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Basic information

Entry
Database: PDB / ID: 7k8h
TitleBeta-lactamase mixed with Ceftriaxone, 50ms
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: 2.60006254355 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)116,20212
Polymers113,6034
Non-polymers2,5988
Water4,450247
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)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)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)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...AA74 - 8048 - 54
12HISHISGLNGLN(chain 'A' and (resid 74 through 80 or resid 82...AA82 - 8356 - 57
13PROPROPROPRO(chain 'A' and (resid 74 through 80 or resid 82...AA85 - 14359 - 117
14GLYGLYASNASN(chain 'A' and (resid 74 through 80 or resid 82...AA146 - 246120 - 220
15ILEILESERSER(chain 'A' and (resid 74 through 80 or resid 82...AA248 - 265222 - 239
26ALAALAVALVAL(chain 'B' and (resid 74 through 80 or resid 82...BB74 - 8048 - 54
27HISHISGLNGLN(chain 'B' and (resid 74 through 80 or resid 82...BB82 - 8356 - 57
28PROPROPROPRO(chain 'B' and (resid 74 through 80 or resid 82...BB85 - 14359 - 117
29GLYGLYASNASN(chain 'B' and (resid 74 through 80 or resid 82...BB146 - 246120 - 220
210ILEILESERSER(chain 'B' and (resid 74 through 80 or resid 82...BB248 - 265222 - 239
311ALAALAVALVAL(chain 'C' and (resid 74 through 80 or resid 82...CC74 - 8048 - 54
312HISHISGLNGLN(chain 'C' and (resid 74 through 80 or resid 82...CC82 - 8356 - 57
313PROPROPROPRO(chain 'C' and (resid 74 through 80 or resid 82...CC85 - 14359 - 117
314GLYGLYASNASN(chain 'C' and (resid 74 through 80 or resid 82...CC146 - 246120 - 220
315ILEILESERSER(chain 'C' and (resid 74 through 80 or resid 82...CC248 - 265222 - 239
416ALAALAVALVAL(chain 'D' and (resid 74 through 80 or resid 82...DD74 - 8048 - 54
417HISHISGLNGLN(chain 'D' and (resid 74 through 80 or resid 82...DD82 - 8356 - 57
418PROPROPROPRO(chain 'D' and (resid 74 through 80 or resid 82...DD85 - 14359 - 117
419GLYGLYASNASN(chain 'D' and (resid 74 through 80 or resid 82...DD146 - 246120 - 220
420ILEILESERSER(chain 'D' and (resid 74 through 80 or resid 82...DD248 - 265222 - 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.: 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.: 247 / 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: 3.77 Å3/Da / Density % sol: 67.33 %
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: 50760 / % possible obs: 100 % / Redundancy: 749 % / CC1/2: 0.97 / Net I/σ(I): 5.5
Reflection shellResolution: 2.6→2.65 Å / Num. unique obs: 2045 / CC1/2: 0.27

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Processing

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

6b5x


Resolution: 2.60006254355→24.8287331207 Å / SU ML: 0.407909873726 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.4108921223
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.275011204447 2218 4.90014139272 %
Rwork0.222726700129 43046 -
obs0.225263796382 45264 87.1937124364 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.3141550322 Å2
Refinement stepCycle: LAST / Resolution: 2.60006254355→24.8287331207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7952 0 164 247 8363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003093910669038280
X-RAY DIFFRACTIONf_angle_d1.3432200876111320
X-RAY DIFFRACTIONf_chiral_restr0.05561711195861280
X-RAY DIFFRACTIONf_plane_restr0.004043124656351504
X-RAY DIFFRACTIONf_dihedral_angle_d13.44973908124924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.65650.418128820662760.3379252915842012X-RAY DIFFRACTION64.2857142857
2.6565-2.71830.452556793672980.3414465667852056X-RAY DIFFRACTION67.3335417318
2.7183-2.78610.408907922059890.336438432431999X-RAY DIFFRACTION65.0669990651
2.7861-2.86140.405451132691230.3303801047561970X-RAY DIFFRACTION64.3208358943
2.8614-2.94540.3728673434241220.3173054436972155X-RAY DIFFRACTION70.6265508685
2.9454-3.04040.3770893374421360.3063544140842478X-RAY DIFFRACTION80.4802955665
3.0404-3.14880.3492727045781350.2922662323032745X-RAY DIFFRACTION89.9718837863
3.1488-3.27460.2970864521791470.250489761212994X-RAY DIFFRACTION97.1243042672
3.2746-3.42330.295192975371830.2399631418693027X-RAY DIFFRACTION99.1658943466
3.4233-3.60330.2332770057871990.2153538380473055X-RAY DIFFRACTION99.8159509202
3.6033-3.82830.2737197840851500.2006390251293069X-RAY DIFFRACTION99.5977722772
3.8283-4.12260.2378646522871520.1841703531533077X-RAY DIFFRACTION99.7220506485
4.1226-4.53520.2242568743791370.1710883877313099X-RAY DIFFRACTION99.6305418719
4.5352-5.18630.2109408792911460.1695208663093106X-RAY DIFFRACTION99.6934396076
5.1863-6.51460.2421896919271740.2000773540263094X-RAY DIFFRACTION99.6645318695
6.5146-24.820.2388933560871510.1968323175513110X-RAY DIFFRACTION97.7811094453

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