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- PDB-1jgt: CRYSTAL STRUCTURE OF BETA-LACTAM SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 1jgt
TitleCRYSTAL STRUCTURE OF BETA-LACTAM SYNTHETASE
ComponentsBETA-LACTAM SYNTHETASE
KeywordsHYDROLASE / BETA-LACTAM SYNTHETASE / ASPARAGINE SYNTHETASE / CLAVULANIC ACID / AMPCPP / CEA / CARBOXYETHYLARGININE
Function / homology
Function and homology information


(carboxyethyl)arginine beta-lactam-synthase / (carboxyethyl)arginine beta-lactam-synthase activity / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / clavulanic acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Glutamine amidotransferase domain / Asparagine synthase / Asparagine synthase / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / HUPs / Nucleophile aminohydrolases, N-terminal / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich ...Glutamine amidotransferase domain / Asparagine synthase / Asparagine synthase / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / HUPs / Nucleophile aminohydrolases, N-terminal / Rossmann-like alpha/beta/alpha sandwich fold / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / N2-(CARBOXYETHYL)-L-ARGININE / Carboxyethyl-arginine beta-lactam-synthase / Carboxyethyl-arginine beta-lactam-synthase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsMiller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of beta-lactam synthetase reveals how to synthesize antibiotics instead of asparagine.
Authors: Miller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C.
History
DepositionJun 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.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.pdbx_leaving_atom_flag / _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_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_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-LACTAM SYNTHETASE
B: BETA-LACTAM SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,21513
Polymers109,2032
Non-polymers2,01211
Water11,205622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-35 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.352, 97.873, 80.969
Angle α, β, γ (deg.)90.00, 90.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAM SYNTHETASE


Mass: 54601.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: 1901 / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(DE3) / References: UniProt: Q9R8E3, UniProt: P0DJQ7*PLUS

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Non-polymers , 5 types, 633 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CMA / N2-(CARBOXYETHYL)-L-ARGININE


Mass: 246.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N4O4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: POLYETHYLENEGLYCOL 4000, GLYCEROL, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 7.5 / Details: Miller, M.T., (2001) Nature Struct. Biol., 8, 684.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
250 mMTris1droppH7.5
37 %(w/v)PEG40001reservoir
4200 mM1reservoirMgCl2
57 %(v/v)glycerol1reservoir
680 mMTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2000
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→19.97 Å / Num. all: 69641 / Num. obs: 68300 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 15.1 Å2 / Limit h max: 31 / Limit h min: -31 / Limit k max: 50 / Limit k min: -31 / Limit l max: 41 / Limit l min: 0 / Observed criterion F max: 569036.55 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.194 / Net I/σ(I): 10.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.23 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 98.3 % / Num. measured all: 465261 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.231

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Processing

Software
NameVersionClassificationNB
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→19.89 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5838 8.8 %RANDOM
Rwork0.195 ---
all0.228 69641 --
obs0.194 66146 95 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 55.1407 Å2 / ksol: 0.386944 e/Å3
Displacement parametersBiso max: 77.68 Å2 / Biso mean: 30.4 Å2 / Biso min: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.39 Å20 Å2-0.27 Å2
2--11.08 Å20 Å2
3----4.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.22 Å
Luzzati d res high-1.95
Refinement stepCycle: LAST / Resolution: 1.95→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7439 0 128 622 8189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23.3
X-RAY DIFFRACTIONx_torsion_impr_deg0.8
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.95-2.040.25461470.25370750.018717768988.2
2.04-2.150.2456497.50.24273770.018695802692.3
2.15-2.280.2236447.40.2274850.0098666812993.8
2.28-2.460.2087538.60.20775320.0088713828595.1
2.46-2.70.277990.20175920.0078693837196.3
2.7-3.090.1968279.50.19676540.0078685848197.7
3.09-3.890.1778109.30.17577510.0068716856198.2
3.89-19.890.1767628.60.17778420.0068834860497.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5bls_new5.parambls_new4.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.254 / % reflection Rfree: 7 % / Rfactor Rwork: 0.253

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