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- PDB-4ewf: The crystal structure of beta-lactamase from Sphaerobacter thermo... -

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Basic information

Entry
Database: PDB / ID: 4ewf
TitleThe crystal structure of beta-lactamase from Sphaerobacter thermophilus DSM 20745
ComponentsBeta-lactamase
KeywordsHYDROLASE / ABA-sandwich / Structural Genomics / Midwest Center for Structural Genomics (MCSG) / PSI-Biology / cytoplasmic
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, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / beta-lactamase
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of beta-lactamase from Sphaerobacter thermophilus DSM 20745
Authors: Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)116,90410
Polymers116,3634
Non-polymers5406
Water7,314406
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2833
Polymers29,0911
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1872
Polymers29,0911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2473
Polymers29,0911
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1872
Polymers29,0911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.500, 215.551, 83.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Beta-lactamase


Mass: 29090.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / Gene: Sthe_2032 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 MAGIC / References: UniProt: D1C5R0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris Propane, NaOH pH 7.0 1.5 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010 / Details: mirrors
RadiationMonochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 84422 / Num. obs: 84422 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.066 / Net I/σ(I): 10.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.84 / Rsym value: 0.682 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→45.328 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2095 4041 4.98 %
Rwork0.181 --
obs0.1824 81065 94.65 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.521 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→45.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 29 406 8235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078006
X-RAY DIFFRACTIONf_angle_d1.08610923
X-RAY DIFFRACTIONf_dihedral_angle_d13.7962894
X-RAY DIFFRACTIONf_chiral_restr0.0721307
X-RAY DIFFRACTIONf_plane_restr0.0051436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.01180.2403610.2047989X-RAY DIFFRACTION36
2.0118-2.03640.2535840.20451766X-RAY DIFFRACTION63
2.0364-2.06220.2221160.21382425X-RAY DIFFRACTION87
2.0622-2.08930.25221220.20712557X-RAY DIFFRACTION93
2.0893-2.11790.22351390.20162634X-RAY DIFFRACTION95
2.1179-2.14820.23581230.19772733X-RAY DIFFRACTION97
2.1482-2.18020.24461350.19922707X-RAY DIFFRACTION98
2.1802-2.21430.23741560.19012734X-RAY DIFFRACTION98
2.2143-2.25060.23421490.1872753X-RAY DIFFRACTION99
2.2506-2.28940.26631420.18982753X-RAY DIFFRACTION99
2.2894-2.3310.23581200.1922803X-RAY DIFFRACTION99
2.331-2.37590.24251440.19112751X-RAY DIFFRACTION99
2.3759-2.42440.22191360.18232782X-RAY DIFFRACTION99
2.4244-2.47710.22971430.18462750X-RAY DIFFRACTION99
2.4771-2.53470.23531550.20572766X-RAY DIFFRACTION99
2.5347-2.59810.26321680.212750X-RAY DIFFRACTION99
2.5981-2.66830.25281360.19972782X-RAY DIFFRACTION100
2.6683-2.74680.24111640.19922758X-RAY DIFFRACTION99
2.7468-2.83550.23441580.20372793X-RAY DIFFRACTION100
2.8355-2.93680.22941550.2052788X-RAY DIFFRACTION100
2.9368-3.05430.2351580.20672810X-RAY DIFFRACTION100
3.0543-3.19330.26251550.2082784X-RAY DIFFRACTION100
3.1933-3.36160.22821330.19582820X-RAY DIFFRACTION100
3.3616-3.57220.21931350.17922813X-RAY DIFFRACTION99
3.5722-3.84780.18081340.15952827X-RAY DIFFRACTION99
3.8478-4.23480.16321720.13672785X-RAY DIFFRACTION99
4.2348-4.8470.13841510.13632813X-RAY DIFFRACTION99
4.847-6.10430.19211520.16792858X-RAY DIFFRACTION99
6.1043-45.33950.16841450.17742740X-RAY DIFFRACTION91
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)
12.3592-0.96720.01991.8279-0.11941.18890.18340.2724-0.0948-0.2475-0.1521-0.0569-0.0082-0.1206-0.02240.12260.03160.03820.1071-0.00190.014928.841110.521527.1073
22.28460.2730.4441.80670.45071.60760.14730.00120.65090.1362-0.1005-0.1743-0.3560.0115-0.02450.30770.04620.10550.1630.02010.290427.712140.061531.4889
30.9727-0.44850.23681.5062-0.29421.782-0.11790.0257-0.01270.0441-0.02380.08670.0876-0.15180.10590.1408-0.05890.08940.216-0.0612-0.0003-4.717427.744748.8223
41.1075-0.3668-0.13872.93470.5221.0022-0.01150.21140.0185-0.22490.056-0.12910.12950.0416-0.03490.1915-0.015-0.0650.2369-0.01120.17495.804578.933749.0208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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