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- PDB-9jg7: Artificial serine-dependent beta-lactamase, S2 -

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Basic information

Entry
Database: PDB / ID: 9jg7
TitleArtificial serine-dependent beta-lactamase, S2
Componentsartificial serine-dependent beta-lactamase
KeywordsELECTRON TRANSPORT / beta-lactamase / oligomeric protein
Function / homologyHEME C / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSong, W.J. / Yu, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2022R1A2C4001207 Korea, Republic Of
CitationJournal: To Be Published
Title: Chemical crossover between metallo- and serine-dependent beta-lactamases
Authors: Song, W.J. / Yu, J.
History
DepositionSep 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: artificial serine-dependent beta-lactamase
C: artificial serine-dependent beta-lactamase
E: artificial serine-dependent beta-lactamase
G: artificial serine-dependent beta-lactamase
I: artificial serine-dependent beta-lactamase
K: artificial serine-dependent beta-lactamase
M: artificial serine-dependent beta-lactamase
O: artificial serine-dependent beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,23043
Polymers94,3468
Non-polymers7,88435
Water8,341463
1
A: artificial serine-dependent beta-lactamase
G: artificial serine-dependent beta-lactamase
K: artificial serine-dependent beta-lactamase
M: artificial serine-dependent beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,31424
Polymers47,1734
Non-polymers4,14120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-227 kcal/mol
Surface area17490 Å2
MethodPISA
2
C: artificial serine-dependent beta-lactamase
E: artificial serine-dependent beta-lactamase
I: artificial serine-dependent beta-lactamase
O: artificial serine-dependent beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,91619
Polymers47,1734
Non-polymers3,74315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-253 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.099, 92.031, 142.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ACEGIKMO

#1: Protein
artificial serine-dependent beta-lactamase


Mass: 11793.220 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 498 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% (v/v) PEG 400, 200mM ammonium acetate, 100mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 66971 / % possible obs: 99.9 % / Redundancy: 14.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.033 / Rrim(I) all: 0.123 / Χ2: 2.03 / Net I/σ(I): 7.6 / Num. measured all: 1210150
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.79-1.8214.71.48741260.7520.9260.4021.5411.453100
1.82-1.8514.71.27841020.7960.9410.3441.3241.489100
1.85-1.8914.71.12741320.850.9580.3041.1671.527100
1.89-1.9314.70.88741310.8920.9710.2390.9191.558100
1.93-1.9714.70.7241420.920.9790.1940.7461.582100
1.97-2.0214.70.63341180.9370.9830.1710.6561.635100
2.02-2.0714.70.47641430.9560.9890.1280.4931.715100
2.07-2.1214.70.36341200.9760.9940.0980.3761.748100
2.12-2.1814.70.30341630.9820.9950.0820.3131.819100
2.18-2.2614.70.25241500.9870.9970.0680.2611.894100
2.26-2.3414.70.22841390.990.9970.0610.2361.879100
2.34-2.4314.70.18741680.9920.9980.050.1941.951100
2.43-2.5414.70.1541700.9950.9990.040.1552.046100
2.54-2.6714.60.1341610.9970.9990.0350.1342.116100
2.67-2.8414.60.10841880.9970.9990.0290.1122.259100
2.84-3.0614.50.08642060.9980.9990.0230.092.514100
3.06-3.3714.40.07742050.99810.0210.082.675100
3.37-3.8614.20.06742180.99910.0180.0692.948100
3.86-4.86140.0642960.99810.0170.0632.909100
4.86-5012.70.06144430.9980.9990.0180.0642.98399.1

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→35.72 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 3387 5.07 %RANDOM
Rwork0.1841 ---
obs0.1866 66819 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 512 464 7584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087286
X-RAY DIFFRACTIONf_angle_d0.919902
X-RAY DIFFRACTIONf_dihedral_angle_d21.7142667
X-RAY DIFFRACTIONf_chiral_restr0.044992
X-RAY DIFFRACTIONf_plane_restr0.0061266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.25641420.20772559X-RAY DIFFRACTION98
1.96-1.990.25431550.20972568X-RAY DIFFRACTION100
1.99-2.020.24371270.20132631X-RAY DIFFRACTION100
2.02-2.050.26771470.20582605X-RAY DIFFRACTION100
2.05-2.090.25121160.19462649X-RAY DIFFRACTION100
2.09-2.130.24111570.18342577X-RAY DIFFRACTION100
2.13-2.170.25641430.17872631X-RAY DIFFRACTION100
2.17-2.210.21751300.17872596X-RAY DIFFRACTION100
2.21-2.260.26251500.18532629X-RAY DIFFRACTION100
2.26-2.310.24141330.1932643X-RAY DIFFRACTION100
2.31-2.370.23461250.18992638X-RAY DIFFRACTION100
2.37-2.430.26811290.19262639X-RAY DIFFRACTION100
2.43-2.50.26241410.18872627X-RAY DIFFRACTION100
2.5-2.590.23411450.1892656X-RAY DIFFRACTION100
2.59-2.680.26951260.19942620X-RAY DIFFRACTION100
2.68-2.780.26721390.212658X-RAY DIFFRACTION100
2.78-2.910.25241500.18932647X-RAY DIFFRACTION100
2.91-3.060.26011310.19652656X-RAY DIFFRACTION100
3.06-3.260.23321450.20452658X-RAY DIFFRACTION100
3.26-3.510.25051390.18862652X-RAY DIFFRACTION100
3.51-3.860.21791560.16932665X-RAY DIFFRACTION100
3.86-4.420.18171450.15872699X-RAY DIFFRACTION100
4.42-5.560.17531460.15972729X-RAY DIFFRACTION100
5.56-35.720.21241700.17862800X-RAY DIFFRACTION99

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