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- PDB-6x9y: The crystal structure of a Beta-lactamase from Escherichia coli CFT073 -

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Basic information

Entry
Database: PDB / ID: 6x9y
TitleThe crystal structure of a Beta-lactamase from Escherichia coli CFT073
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S,R MESO-TARTARIC ACID / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTan, K. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of a Beta-lactamase from Escherichia coli CFT073
Authors: Tan, K. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)80,99415
Polymers79,7192
Non-polymers1,27513
Water4,324240
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4207
Polymers39,8591
Non-polymers5616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5748
Polymers39,8591
Non-polymers7157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.176, 128.176, 92.761
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Beta-lactamase /


Mass: 39859.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Strain: CFT073 / ATCC 700928 / UPEC / Gene: ampC, c5238 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H2VDE7, UniProt: P00811*PLUS, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium Acetate, 0.1 M HEPES: NaOH, 25 % (w/v) PEG 4000, 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.9→47.6 Å / Num. obs: 68159 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 31.5729232094 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Χ2: 1.086 / Net I/σ(I): 27.58
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 3396 / CC1/2: 0.851 / CC star: 0.959 / Rpim(I) all: 0.296 / Rrim(I) all: 0.77 / Χ2: 0.484 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.6 Å / SU ML: 0.178693821941 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.1759964247
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3325 4.88 %random
Rwork0.161 64790 --
obs0.162 68115 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.49 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5579 0 77 240 5896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212771725565813
X-RAY DIFFRACTIONf_angle_d1.154327862127939
X-RAY DIFFRACTIONf_chiral_restr0.0744872545217860
X-RAY DIFFRACTIONf_plane_restr0.007716681425041014
X-RAY DIFFRACTIONf_dihedral_angle_d13.85178003043404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92350.2709512972481370.216512464962265X-RAY DIFFRACTION83.986013986
1.9235-1.95220.2807973767461340.1994928366962702X-RAY DIFFRACTION100
1.9522-1.98270.2320440998221410.1839983583492689X-RAY DIFFRACTION99.8588567396
1.9827-2.01520.2135465448031440.1857341005622699X-RAY DIFFRACTION99.9297012302
2.0152-2.04990.2123371214191360.1720830736192721X-RAY DIFFRACTION100
2.0499-2.08720.2549103043561730.168238960282671X-RAY DIFFRACTION99.9648506151
2.0872-2.12740.203271257421180.1655454555572723X-RAY DIFFRACTION99.9648135116
2.1274-2.17080.2034531224771340.1603312144652741X-RAY DIFFRACTION100
2.1708-2.2180.2082090945941260.1557364935122686X-RAY DIFFRACTION99.9644507643
2.218-2.26960.1931758113171560.1570593809752699X-RAY DIFFRACTION100
2.2696-2.32630.2211868534721450.1592919628212732X-RAY DIFFRACTION99.9652536484
2.3263-2.38920.1912673084741430.165144351182697X-RAY DIFFRACTION99.9296270232
2.3892-2.45950.177289993151270.1674534983162710X-RAY DIFFRACTION99.9647639183
2.4595-2.53890.2042291168521310.1665259770592710X-RAY DIFFRACTION99.9648135116
2.5389-2.62960.2303661062491110.174197400992753X-RAY DIFFRACTION100
2.6296-2.73490.2254743863621520.1773643897472722X-RAY DIFFRACTION100
2.7349-2.85940.2188028700121400.1825355772382692X-RAY DIFFRACTION99.9294283698
2.8594-3.01010.249543405411200.1835112257222738X-RAY DIFFRACTION100
3.0101-3.19870.2133463360961320.1771312211912737X-RAY DIFFRACTION99.8955431755
3.1987-3.44560.2029042739441520.1826447453042720X-RAY DIFFRACTION100
3.4456-3.79220.1838776852491270.1545339948722729X-RAY DIFFRACTION100
3.7922-4.34060.1742091795281480.1408224675392733X-RAY DIFFRACTION99.9306278182
4.3406-5.46740.1850994132211500.1317497435292748X-RAY DIFFRACTION99.9655053467
5.4674-47.60.1585352884061480.1455779343612773X-RAY DIFFRACTION99.5229982964
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.768348188911.216583004590.8511496311783.279747638445.077893517258.21396378185-0.272658919052-0.6898141663610.3761711003661.054226550330.674151679406-1.53995063032-0.1303269058080.820715866651-0.3727746172130.3660628211720.00102654967143-0.1877782873480.575663957256-0.04167681061260.6968538464516.3753966503-46.83699821616.8821594071
22.84581649265-1.375782541660.007414107002632.328454018930.06762279074190.6098969903640.2411362344430.1543590034990.275490419287-0.291014886294-0.207973210429-0.50855577055-0.04191595290410.0446578043554-0.01126403365720.2770341415770.001548570346050.09153746425350.2609997625150.06127423405360.3075787968054.60377763494-44.1947511239-2.87828516589
33.13343028921-0.26680115518-0.4395829877933.690096206170.3809247800183.158609163150.1876666928610.556528146909-0.602521765242-0.489523319772-0.1788748240440.3335040943580.206112879713-0.1275004933110.02001497794430.2572169385430.0543632401005-0.06002945969570.312063157097-0.07725305843110.296507921056-13.2125847418-54.4934495381-9.13440381144
42.83891450629-1.023088768830.06331243727142.386065702570.4050037000280.6248667645250.11918937770.06990481205260.22266161321-0.123549418822-0.0959463358703-0.47326253988-0.1206315087670.0363720498078-0.02208239984760.232748012747-0.01404204132030.03759536573470.2267678755760.04218329039940.255949499131.3133873586-43.82657901631.6538788576
53.738618697023.71803190124-4.228694433016.81733128794-1.931104198398.70461157760.7056192341761.298986133971.52259317365-0.814057998498-0.09323378225090.265254831554-0.9204542967510.00404661503494-0.4644227822550.5901171201670.1588153588910.06074854157370.4371292319530.1589818264690.670522052721-46.8946653028-10.0758623944-16.634838058
63.03764607853-0.9099461859690.1538175827511.599969145480.01152240222731.010719971280.0142425841739-0.1566823102180.959068505331-0.04002327533290.0633338490377-0.107836337803-0.250929161139-0.00549267078073-0.0839475577070.310740215996-0.0100125627750.02718729187410.235343351181-0.06603362202290.547282426671-43.3875041038-12.7293890911-1.23705993864
73.28525367819-0.305058949217-0.01097458574193.012143252070.548203637341.82343181062-0.189483837096-0.828073923394-0.1600470308520.4586792552830.2177914576940.232644502290.01136696899860.1382570561040.006128466686850.2806902554040.07106291283280.02373912911580.4212710703970.01161113655160.191506731392-37.0455849846-36.993354310711.7344788403
83.57010504486-0.9380830080220.1025745838021.89011868911-0.2926132718140.928970948047-0.0637391370671-0.7760335199840.9383952630690.2174681173140.2431549094150.00639163589355-0.1776876787360.0202232291893-0.1563439627140.401675550160.01313692457990.02436288465720.395577293982-0.221138124160.609729212266-46.3978926737-13.11864651378.51945440446
93.15062642108-1.17582389556-0.3791227050452.18936736586-0.08732888642670.7669747562170.1029648135930.0241738372340.502258688113-0.15800333047-0.0218505469634-0.144776723433-0.1035635991770.117214990606-0.08377592885690.236726432984-0.00826983065517-0.003221446231750.234537571094-0.01882652636140.236310963528-36.4347183516-24.1810456903-5.34270669293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 189 )
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 388 )
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 50 )
6X-RAY DIFFRACTION6chain 'B' and (resid 51 through 106 )
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 204 )
8X-RAY DIFFRACTION8chain 'B' and (resid 205 through 236 )
9X-RAY DIFFRACTION9chain 'B' and (resid 237 through 388 )

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