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- PDB-6wgq: The crystal structure of a beta-lactamase from Shigella flexneri ... -

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Basic information

Entry
Database: PDB / ID: 6wgq
TitleThe crystal structure of a beta-lactamase from Shigella flexneri 2a str. 2457T
ComponentsBeta-lactamase
KeywordsHYDROLASE / 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
FORMIC ACID / NICKEL (II) ION / Beta-lactamase / Beta-lactamase
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 Shigella flexneri 2a str. 2457T
Authors: Tan, K. / Wu, R. / Endres, M. / Joachimiak, A.
History
DepositionApr 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)81,86231
Polymers79,4502
Non-polymers2,41129
Water9,674537
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,42121
Polymers39,7251
Non-polymers1,69620
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,44110
Polymers39,7251
Non-polymers7169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.419, 73.767, 109.512
Angle α, β, γ (deg.)90.000, 92.397, 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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase / / Beta-lactamase penicillin resistance


Mass: 39725.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ampC, S4573, SAMEA3710568_04045 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: A0A4S3P3Z5, UniProt: A0A0H2V5I6*PLUS, beta-lactamase

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Non-polymers , 6 types, 566 molecules

#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES:NaOH 30% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→46.4 Å / Num. obs: 66678 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 18.81 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.067 / Rrim(I) all: 0.134 / Χ2: 1.65 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2899 / CC1/2: 0.661 / CC star: 0.892 / Rpim(I) all: 0.377 / Rrim(I) all: 0.68 / Χ2: 0.806 / % possible all: 86.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.17.1_3660refinement
HKL-3000phasing
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DPZ

6dpz


Resolution: 1.8→46.38 Å / SU ML: 0.1561 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.1507
RfactorNum. reflection% reflection
Rfree0.1916 3315 4.97 %
Rwork0.1527 --
obs0.1546 66647 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.86 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 138 538 6245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685881
X-RAY DIFFRACTIONf_angle_d0.85568017
X-RAY DIFFRACTIONf_chiral_restr0.0565857
X-RAY DIFFRACTIONf_plane_restr0.00621025
X-RAY DIFFRACTIONf_dihedral_angle_d14.4822147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.23441300.19132032X-RAY DIFFRACTION77.05
1.83-1.860.23951390.19112473X-RAY DIFFRACTION90.85
1.86-1.880.22941410.18382568X-RAY DIFFRACTION96.23
1.89-1.920.23651530.18362617X-RAY DIFFRACTION99.6
1.92-1.950.22921490.17432685X-RAY DIFFRACTION99.4
1.95-1.980.19211520.15732650X-RAY DIFFRACTION99.4
1.98-2.020.20441470.15972653X-RAY DIFFRACTION99.36
2.02-2.060.19581460.15842650X-RAY DIFFRACTION99.01
2.06-2.110.19621520.15922659X-RAY DIFFRACTION98.98
2.11-2.160.1871400.15632643X-RAY DIFFRACTION98.83
2.16-2.210.20111400.15332690X-RAY DIFFRACTION98.88
2.21-2.270.21421310.14872661X-RAY DIFFRACTION99.61
2.27-2.340.19991430.15372684X-RAY DIFFRACTION99.51
2.34-2.410.20121480.1562679X-RAY DIFFRACTION99.51
2.41-2.50.23251340.15442669X-RAY DIFFRACTION99.43
2.5-2.60.22491270.16052689X-RAY DIFFRACTION98.98
2.6-2.720.21471160.16852709X-RAY DIFFRACTION98.6
2.72-2.860.19991240.16432689X-RAY DIFFRACTION99.68
2.86-3.040.18161360.16382681X-RAY DIFFRACTION99.4
3.04-3.280.17481430.16522680X-RAY DIFFRACTION99.02
3.28-3.610.18921480.14642660X-RAY DIFFRACTION98.25
3.61-4.130.16491270.13352717X-RAY DIFFRACTION99.48
4.13-5.20.1471160.12322731X-RAY DIFFRACTION98.79
5.2-46.380.16951330.1442763X-RAY DIFFRACTION98.7
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)
15.532576556197.09492003992-4.653539330059.44169904743-6.003148713834.04353057964-0.3742738042940.297136101612-0.30806828256-0.6051259572170.154811349612-0.3658519227740.3550425669220.2564230533390.2814968951810.222206415978-0.00736535069120.01548135093670.235212183241-0.006081553113830.2048809842551.62937770101-10.765432474126.0424363819
20.6037983091450.09185822710570.01627367101320.9419763585780.3319057880031.904782183950.01368013564870.03076154094690.005440502897960.00616119424768-0.02201555685980.0377805574827-0.0144675316244-0.1134842084250.02339927443550.07709903713610.00158413750819-0.01045584519950.108058323050.02505565295360.136031972741-10.68246993942.3814206826841.203323667
31.79003693516-0.4178329184960.2086829310521.864356588680.1120624565262.259636199730.0295806918186-0.108480483393-0.06264870456360.0722109858079-0.01778106038980.1836737401470.0645327163565-0.292241449439-0.009708305663060.155589993392-0.01249326747870.01932019828110.1688429261750.01330043450850.128032685662-16.5644871065-1.94458783461.2946768388
41.261835531160.2750268185060.2392472986311.344608326560.4834056552881.454396170276.92469606591E-50.01994873995060.03668537437860.0416105747221-0.03024574408650.142334848125-0.038109832241-0.2105609408460.03302958110580.1304486008890.00917287300016-0.009377281335590.1476882888550.0180025783680.15222494047-16.72000056574.6603699684839.1839699674
51.42495466492-1.891299601490.9353153967133.674478644370.0669268184251.525494850830.02932753445770.08274344050760.0757909810579-0.0769202337139-0.119528397171-0.325543800238-0.07500720171020.1389471245720.1080381073020.0765792016273-0.007336690636510.01142400704030.11662502198-0.007502789869150.1225250593780.8919261808475.3421651094849.9603767294
60.3194673274470.1502483952960.1531692336790.9069388189940.1064091181841.62803317444-0.0383237334323-0.01145092972140.006912418470.02708936279850.0262879020496-0.0709175684930.1160939598910.1233224714980.009584784871380.1035169634330.0156802983514-0.006685937071830.1176566333450.009239638011190.1556703355110.237376618104-6.4743409423443.8970949241
76.82211115917-6.687231048914.601931922297.30515170766-5.459967109664.48932652073-0.343324488908-0.6386180579820.389356010680.5199037842140.252702333149-0.408352348516-0.733266383890.4129574441680.3437656904040.357694479104-0.03647974846610.003663207632490.245046897358-0.0179163419250.2441314120011.9455382965131.345562562728.7126587595
80.736635531673-0.101653595847-0.03533149146672.069182634590.90012851712.61317004989-0.00917885605938-0.0950672748380.05278701248720.143357236976-0.00198682065430.0857525185831-0.125012928009-0.1479979138550.02096573604190.1113802751950.004114061484160.02463240637590.1213543572090.02697904615420.128700802737-8.5525032370721.247855276321.2569830201
91.478015165570.109706242325-0.3957110385443.32516347689-0.4958990847333.013990381650.06265334912370.310825674913-0.0245175053209-0.579207407291-0.06118598559670.2873543170190.165296648934-0.234600522957-0.0003352203516860.290776875788-0.00488521987453-0.03789262170010.246814454987-0.01262517774940.16041076025-10.529741722214.0809289947-10.2486647129
103.301529415211.12432728094-0.05380575209543.6226707083-0.4259533908812.18454536842-0.0532310137110.2275675587420.252063699451-0.2420736325320.1203856806770.427765091516-0.0681093604078-0.467948241677-0.05515849699980.1981226373930.0253285928192-0.03145734927270.2388882032280.02734536482310.14505373682-15.570401536223.7107747125-6.53383769794
111.46426911073-0.468856957677-0.1608298400561.395138345470.4281193439121.89725797161-0.0026465452674-0.005183687312710.0037373364099-0.0131359657356-0.006047117488670.209897230980.0085493775505-0.2991102434250.01041006545820.142000863259-0.006340452494420.01181338102540.169879618960.02150393828730.157537524485-15.584163741415.822444487314.4047120159
122.459816179992.43686404293-0.9865017954655.407896594950.07751290552771.401002002720.0234008693401-0.0819187072686-0.1275660044650.107831419207-0.158535020302-0.4489398492910.06284666719340.0970276401720.1353836471380.1188022865170.01203162168960.006329793923660.132858111427-0.00781362459830.1264145420492.7340904707714.27859594795.08765294731
131.18288212806-0.656889051165-0.709081033971.921244025180.1246596280392.43389292836-0.02507663409380.008445892539710.023295330214-0.08696781408610.0503927117263-0.168904588574-0.1234625347680.165201434128-0.0239009455330.144163267732-0.02029651627850.006420832415780.114355678193-0.002177977017540.1449501171682.8962061109125.5558658616.95292083148
144.160981140740.3334468898570.5555129573135.31588896342-1.231846710214.491569795740.0526407358281-0.02073208223280.129369925594-0.0715833450072-0.070905385574-0.269406531685-0.3250197835980.361887849950.01291109785480.174525281608-0.03072570536780.01281805354550.118806081525-0.01945464361070.0668496001680.44555630909628.383422410818.6759991955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 178 )
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 291 )
6X-RAY DIFFRACTION6chain 'A' and (resid 292 through 377 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 39 )
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 95 )
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 131 )
10X-RAY DIFFRACTION10chain 'B' and (resid 132 through 178 )
11X-RAY DIFFRACTION11chain 'B' and (resid 179 through 253 )
12X-RAY DIFFRACTION12chain 'B' and (resid 254 through 291 )
13X-RAY DIFFRACTION13chain 'B' and (resid 292 through 348 )
14X-RAY DIFFRACTION14chain 'B' and (resid 349 through 377 )

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