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- PDB-1m1z: BETA-LACTAM SYNTHETASE APO ENZYME -

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Basic information

Entry
Database: PDB / ID: 1m1z
TitleBETA-LACTAM SYNTHETASE APO ENZYME
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
Carboxyethyl-arginine beta-lactam-synthase / Carboxyethyl-arginine beta-lactam-synthase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionJun 20, 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 1.3Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAM SYNTHETASE
B: BETA-LACTAM SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)109,2032
Polymers109,2032
Non-polymers00
Water10,863603
1
A: BETA-LACTAM SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)54,6021
Polymers54,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAM SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)54,6021
Polymers54,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.179, 97.469, 80.968
Angle α, β, γ (deg.)90.00, 90.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: taxon: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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.24 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Magnesium Chloride, 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: 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: 1.95→25 Å / Num. all: 69211 / Num. obs: 64182 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.051 / Net I/σ(I): 18.01
Reflection shellResolution: 1.95→2.02 Å / Rsym value: 0.253 / % possible all: 90
Reflection
*PLUS
Lowest resolution: 24 Å / Num. obs: 69211 / Num. measured all: 690463 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.253

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Processing

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

1jgt


Resolution: 1.95→23.88 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 5821 9.2 %RANDOM
Rwork0.197 ---
all-63190 --
obs-63190 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5661 Å2 / ksol: 0.364086 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å2-1.72 Å2
2--5.47 Å20 Å2
3----3.88 Å2
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.95→23.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 0 0 603 7883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 909 9 %
Rwork0.241 9176 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 24 Å / % reflection Rfree: 9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2

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