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- PDB-1upc: Carboxyethylarginine synthase from Streptomyces clavuligerus -

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Basic information

Entry
Database: PDB / ID: 1upc
TitleCarboxyethylarginine synthase from Streptomyces clavuligerus
ComponentsCARBOXYETHYLARGININE SYNTHASE
KeywordsSYNTHASE / CLAVULANIC ACID / ANTIBIOTIC / LACTAMASE / FLAVOPROTEIN / THIAMINE PYROPHOSPHATE
Function / homology
Function and homology information


N2-(2-carboxyethyl)arginine synthase / N2-(2-carboxyethyl)arginine synthase activity / acetolactate synthase complex / acetolactate synthase activity / L-valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / flavin adenine dinucleotide binding / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains ...Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / N(2)-(2-carboxyethyl)arginine synthase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCaines, M.E.C. / Elkins, J.M. / Hewitson, K.S. / Schofield, C.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure and Mechanistic Implications of N2-(2-Carboxyethyl)Arginine Synthase, the First Enzyme in the Clavulanic Acid Biosynthesis Pathway
Authors: Caines, M.E.C. / Elkins, J.M. / Hewitson, K.S. / Schofield, C.J.
History
DepositionSep 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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: CARBOXYETHYLARGININE SYNTHASE
B: CARBOXYETHYLARGININE SYNTHASE
C: CARBOXYETHYLARGININE SYNTHASE
D: CARBOXYETHYLARGININE SYNTHASE
E: CARBOXYETHYLARGININE SYNTHASE
F: CARBOXYETHYLARGININE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,63930
Polymers365,7896
Non-polymers3,85024
Water15,349852
1
A: CARBOXYETHYLARGININE SYNTHASE
B: CARBOXYETHYLARGININE SYNTHASE
C: CARBOXYETHYLARGININE SYNTHASE
D: CARBOXYETHYLARGININE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,42620
Polymers243,8594
Non-polymers2,56716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: CARBOXYETHYLARGININE SYNTHASE
F: CARBOXYETHYLARGININE SYNTHASE
hetero molecules

E: CARBOXYETHYLARGININE SYNTHASE
F: CARBOXYETHYLARGININE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,42620
Polymers243,8594
Non-polymers2,56716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.073, 187.196, 198.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SO4 / End label comp-ID: SO4 / Refine code: 4 / Auth seq-ID: 12 - 603 / Label seq-ID: 12

Dom-IDAuth asym-IDLabel asym-ID
1AA - J
2BB - N
3CC - R
4DD - V
5EE - Z
6FF - DA

NCS oper:
IDCodeMatrixVector
1given(0.80258, 0.56804, -0.18219), (0.56821, -0.82094, -0.05648), (-0.18165, -0.05819, -0.98164)-18.96071, 83.23276, 71.33143
2given(-0.81035, -0.58238, 0.06456), (-0.58297, 0.79024, -0.18883), (0.05896, -0.19066, -0.97988)48.43149, 23.77948, 74.68426
3given(-0.99276, 0.01323, 0.1194), (0.01623, -0.97003, 0.24246), (0.11903, 0.24264, 0.96279)19.97463, 87.35296, -12.03426
4given(-0.26617, -0.95379, 0.13938), (0.96186, -0.27227, -0.0263), (0.06304, 0.12706, 0.98989)44.89922, 2.22933, 63.91455
5given(-0.7796, 0.6255, -0.03112), (0.62365, 0.77082, -0.12996), (-0.0573, -0.12072, -0.99103)-19.70426, -40.81025, 143.64339

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Components

#1: Protein
CARBOXYETHYLARGININE SYNTHASE


Mass: 60964.828 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET24A(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LCV9
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / 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: 2.96 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.5
Details: 1.6M (NH4)2SO4, 0.1M HEPES PH7.4. 10 MG/ML PROTEIN WITH 3-FOLD EXCESS OF TDP., pH 7.50
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
30.1 MHEPES1reservoirpH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.45→35.05 Å / Num. obs: 168019 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.7
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 35.05 Å / Redundancy: 4.1 % / Num. measured all: 683385 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 98.9 % / Redundancy: 3.8 % / Num. unique obs: 24074 / Num. measured obs: 92570 / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→38 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.764 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 8434 5 %RANDOM
Rwork0.176 ---
obs0.178 159529 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--1.65 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.45→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25009 0 222 852 26083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02125788
X-RAY DIFFRACTIONr_bond_other_d0.0020.0223660
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9635244
X-RAY DIFFRACTIONr_angle_other_deg0.867354731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.24046
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0229207
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025102
X-RAY DIFFRACTIONr_nbd_refined0.2090.25533
X-RAY DIFFRACTIONr_nbd_other0.2370.227474
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.214238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.21054
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5451.516677
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.991226817
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.44839111
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4574.58427
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8025 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.210.5
2Bmedium positional0.230.5
3Cmedium positional0.210.5
4Dmedium positional0.160.5
5Emedium positional0.180.5
6Fmedium positional0.180.5
1Amedium thermal0.572
2Bmedium thermal1.022
3Cmedium thermal0.842
4Dmedium thermal0.732
5Emedium thermal0.792
6Fmedium thermal0.592
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 618
Rwork0.224 11439
Refinement
*PLUS
Lowest resolution: 35.05 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.47

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