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- PDB-1mb9: BETA-LACTAM SYNTHETASE COMPLEXED WITH ATP -

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Basic information

Entry
Database: PDB / ID: 1mb9
TitleBETA-LACTAM SYNTHETASE COMPLEXED WITH ATP
ComponentsBETA-LACTAM SYNTHETASE
KeywordsHYDROLASE / CLAVULANIC ACID / ASPARAGINE SYNTHETASE / BETA-LACTAM SYNTHETASE / CARBOXYETHYL ARGININE / DEOXYGUANIDINOPROCLAVAMINIC ACID
Function / homology
Function and homology information


(carboxyethyl)arginine beta-lactam-synthase / (carboxyethyl)arginine beta-lactam-synthase activity / asparagine synthase (glutamine-hydrolyzing) activity / : / clavulanic acid biosynthetic process / ATP binding / metal ion binding / cytosol
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 ...: / 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
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PYROPHOSPHATE 2- / Carboxyethyl-arginine beta-lactam-synthase / Carboxyethyl-arginine beta-lactam-synthase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMiller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The catalytic cycle of beta -lactam synthetase observed by x-ray crystallographic snapshots
Authors: Miller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C.
History
DepositionAug 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: 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 / 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_ptnr2_label_alt_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_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
Remark 600HETEROGEN ATP 701 HAS AN ALTERNATE CONFORMATION 'A'. AMP 706 AND POP 705 HAS ALTERNATE CONFORMATION 'B'.

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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)110,83810
Polymers109,2032
Non-polymers1,6358
Water8,467470
1
A: BETA-LACTAM SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6816
Polymers54,6021
Non-polymers1,0795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAM SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1574
Polymers54,6021
Non-polymers5563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.252, 97.571, 81.313
Angle α, β, γ (deg.)90.00, 90.69, 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, 478 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 44.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, Magnesium Chloride, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / 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: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2000
RadiationMonochromator: Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→25 Å / Num. all: 64591 / Num. obs: 54280 / % possible obs: 99.6 % / Observed criterion σ(I): 5 / Biso Wilson estimate: 7.1 Å2 / Rsym value: 0.084
Reflection shellResolution: 2.11→2.19 Å / Rsym value: 0.296 / % possible all: 98.5
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 25 Å / Num. measured all: 594199 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.296

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JGT

1jgt


Resolution: 2.11→24.78 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4774 9 %RANDOM
Rwork0.21 ---
all-54912 --
obs-53056 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.97 Å2 / ksol: 0.378188 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.04 Å20 Å2-1.77 Å2
2--10.27 Å20 Å2
3----5.23 Å2
Refine analyzeLuzzati coordinate error free: 0.3 Å / Luzzati sigma a free: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.11→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 98 470 7960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d2.67
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 2.11→2.24 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 647 7.8 %
Rwork0.243 7614 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4LIGAND_0723.PARAMLIGAND_0723.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.67

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