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- PDB-7cin: Crystal structure of the extended-spectrum class C beta-lactamase... -

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Basic information

Entry
Database: PDB / ID: 7cin
TitleCrystal structure of the extended-spectrum class C beta-lactamase AmpC BER with the ordered R2 loop
ComponentsBeta-lactamase
KeywordsHYDROLASE / Class C beta-lactamase / wild-type AmpC BER / two amino acid insertion in the R2 loop / ordered R2 loop
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic / nucleotide binding
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79006366468 Å
AuthorsJeong, B.G. / Cha, S.S.
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Crystal structure of AmpC BER and molecular docking lead to the discovery of broad inhibition activities of halisulfates against beta-lactamases.
Authors: Jeong, B.G. / Na, J.H. / Bae, D.W. / Park, S.B. / Lee, H.S. / Cha, S.S.
History
DepositionJul 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4005
Polymers81,1122
Non-polymers2883
Water9,728540
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7483
Polymers40,5561
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area14950 Å2
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6522
Polymers40,5561
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.854, 64.484, 176.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11ILEILEHISHIS(chain A and (resseq 5:10 or resseq 12:193 or resseq...AA5 - 1011 - 16
12THRTHRGLUGLU(chain A and (resseq 5:10 or resseq 12:193 or resseq...AA12 - 19318 - 199
13ASNASNPROPRO(chain A and (resseq 5:10 or resseq 12:193 or resseq...AA195 - 237201 - 243
14ASPASPASPASP(chain A and (resseq 5:10 or resseq 12:193 or resseq...AA239 - 242245 - 248
15THRTHRILEILE(chain A and (resseq 5:10 or resseq 12:193 or resseq...AA244 - 249250 - 255
16LEULEUASPASP(chain A and (resseq 5:10 or resseq 12:193 or resseq...AA251 - 278257 - 284
17ALAALAVALVAL(chain A and (resseq 5:10 or resseq 12:193 or resseq...AA293 - 297299 - 303
18ALAALAGLNGLN(chain A and (resseq 5:10 or resseq 12:193 or resseq...AA299 - 360305 - 366
29ILEILEHISHIS(chain B and (resseq 5:10 or resseq 12:193 or resseq...BB5 - 1011 - 16
210THRTHRGLUGLU(chain B and (resseq 5:10 or resseq 12:193 or resseq...BB12 - 19318 - 199
211ASNASNPROPRO(chain B and (resseq 5:10 or resseq 12:193 or resseq...BB195 - 237201 - 243
212ASPASPASPASP(chain B and (resseq 5:10 or resseq 12:193 or resseq...BB239 - 242245 - 248
213THRTHRILEILE(chain B and (resseq 5:10 or resseq 12:193 or resseq...BB244 - 249250 - 255
214LEULEUASPASP(chain B and (resseq 5:10 or resseq 12:193 or resseq...BB251 - 278257 - 284
215ALAALAVALVAL(chain B and (resseq 5:10 or resseq 12:193 or resseq...BB293 - 297299 - 303
216ALAALAGLNGLN(chain B and (resseq 5:10 or resseq 12:193 or resseq...BB299 - 360305 - 366

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Components

#1: Protein Beta-lactamase


Mass: 40556.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ampC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7TUE6, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.13 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.2M lithium sulfate, 0.1M bis-tris pH 5.5, 25% polyethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 63935 / % possible obs: 96.4 % / Redundancy: 9.2 % / Biso Wilson estimate: 17.5929799864 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 48.62
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.766 / Num. unique obs: 2979 / Rsym value: 0.24 / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
Coot0.8.9model building
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ggw

5ggw


Resolution: 1.79006366468→44.257948039 Å / SU ML: 0.202379179681 / Cross valid method: THROUGHOUT / σ(F): 1.57959246439 / Phase error: 18.9390301581
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.211489334734 3247 5.08177478676 %
Rwork0.171071912642 60648 -
obs0.173138661665 63895 96.408902301 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.0000327727 Å2
Refinement stepCycle: LAST / Resolution: 1.79006366468→44.257948039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 15 540 6069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005877633500245696
X-RAY DIFFRACTIONf_angle_d0.8525390500217784
X-RAY DIFFRACTIONf_chiral_restr0.0551029486595835
X-RAY DIFFRACTIONf_plane_restr0.006484508205381001
X-RAY DIFFRACTIONf_dihedral_angle_d10.50910473033346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7901-1.81680.2820104953011460.2360647291042462X-RAY DIFFRACTION92.7453769559
1.8168-1.84520.2722035024531460.2252698967482488X-RAY DIFFRACTION91.4901007294
1.8452-1.87540.2960649601161140.213551539582489X-RAY DIFFRACTION93.3979189092
1.8754-1.90780.2678587656631260.2031779899532532X-RAY DIFFRACTION92.452173913
1.9078-1.94250.2559034725941370.1887613002542538X-RAY DIFFRACTION95.1957295374
1.9425-1.97980.2184858040191410.1757549104562558X-RAY DIFFRACTION94.2388268156
1.9798-2.02020.2059403081951370.1725075059652580X-RAY DIFFRACTION94.6030640669
2.0202-2.06420.2044099197131340.1759788080712591X-RAY DIFFRACTION96.1199294533
2.0642-2.11220.2049697915481300.1729716968312576X-RAY DIFFRACTION95.1476793249
2.1122-2.1650.2181727644751250.1683915808132638X-RAY DIFFRACTION95.9375
2.165-2.22350.2113601790461230.1660288712832626X-RAY DIFFRACTION96.3547143358
2.2235-2.28890.2288136044561510.1669813267172592X-RAY DIFFRACTION96.8573446328
2.2889-2.36280.2168767366491500.1693168926442623X-RAY DIFFRACTION96.8564442892
2.3628-2.44730.2078221077111220.1608968620552653X-RAY DIFFRACTION96.2539021852
2.4473-2.54520.2074905038931480.1650437617092630X-RAY DIFFRACTION96.3913948647
2.5452-2.66110.2023216502441410.1808452087382652X-RAY DIFFRACTION97.0802919708
2.6611-2.80130.2452986277241560.1841619459162680X-RAY DIFFRACTION98.2334603395
2.8013-2.97680.2606418449451570.1926474134192715X-RAY DIFFRACTION99.2055267703
2.9768-3.20660.2397964190371570.1871729988552737X-RAY DIFFRACTION99.7587038952
3.2066-3.52920.2081702778971420.1710442022452762X-RAY DIFFRACTION99.7595328066
3.5292-4.03960.1767776208091580.1471224351682789X-RAY DIFFRACTION99.8306233062
4.0396-5.08820.1590856100371570.1370361011542804X-RAY DIFFRACTION99.8987854251
5.0882-44.2579480390.185823787411490.1660832595722933X-RAY DIFFRACTION98.9723827874

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