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- PDB-2ihv: Carboxyethylarginine synthase from Streptomyces clavuligerus: 5-g... -

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Basic information

Entry
Database: PDB / ID: 2ihv
TitleCarboxyethylarginine synthase from Streptomyces clavuligerus: 5-guanidinovaleric acid complex
ComponentsCarboxyethylarginine synthase
KeywordsTRANSFERASE / Thiamin diphosphate complex
Function / homology
Function and homology information


N2-(2-carboxyethyl)arginine synthase / N2-(2-carboxyethyl)arginine synthase activity / thiamine pyrophosphate 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
5-{[AMINO(IMINO)METHYL]AMINO}PENTANOIC ACID / : / THIAMINE DIPHOSPHATE / N(2)-(2-carboxyethyl)arginine synthase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCaines, M.E. / Schofield, C.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structural and mechanistic studies on N(2)-(2-carboxyethyl)arginine synthase.
Authors: Caines, M.E. / Sorensen, J.L. / Schofield, C.J.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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_asym_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.end_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,52922
Polymers243,8594
Non-polymers2,67018
Water17,835990
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.744, 128.297, 197.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLUAA11 - 26211 - 262
21LYSLYSGLUGLUBB11 - 26211 - 262
31LYSLYSGLUGLUCC11 - 26211 - 262
41LYSLYSGLUGLUDD11 - 26211 - 262
52THRTHRILEILEAA283 - 573283 - 573
62THRTHRILEILEBB283 - 573283 - 573
72THRTHRTYRTYRCC283 - 561283 - 561
82THRTHRILEILEDD283 - 573283 - 573

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carboxyethylarginine synthase


Mass: 60964.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: ceas2 / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9LCV9, N2-(2-carboxyethyl)arginine synthase

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Non-polymers , 5 types, 1008 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical
ChemComp-GVA / 5-{[AMINO(IMINO)METHYL]AMINO}PENTANOIC ACID / 5-GUANIDINOVALERIC ACID


Mass: 159.186 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13N3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 990 / 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: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.6 M (NH4)2SO4, 0.1 M HEPES pH 7.4, 10 mg/mL protein with 3-fold excess of ThDP, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Nov 10, 2004
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 136572 / Num. obs: 131792 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 30.122 Å2 / Rmerge(I) obs: 0.115 / Χ2: 0.965 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.347 / Num. unique all: 12059 / Χ2: 0.976 / % possible all: 89.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UPA

1upa


Resolution: 2.3→49.15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.618 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.192 6386 4.8 %RANDOM
Rwork0.161 ---
all0.161 136478 --
obs0.162 131701 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.165 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--1.17 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16854 0 158 990 18002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02217197
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.96823530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02952244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20323.572697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.926152467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.715112
X-RAY DIFFRACTIONr_chiral_restr0.0840.22725
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213280
X-RAY DIFFRACTIONr_nbd_refined0.1890.27584
X-RAY DIFFRACTIONr_nbtor_refined0.2980.211731
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.21086
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.23
X-RAY DIFFRACTIONr_mcbond_it0.4521.511192
X-RAY DIFFRACTIONr_mcangle_it0.854218001
X-RAY DIFFRACTIONr_scbond_it1.3336058
X-RAY DIFFRACTIONr_scangle_it2.1894.55526
Refine LS restraints NCS

Ens-ID: 1 / Number: 3902 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.170.5
2BMEDIUM POSITIONAL0.180.5
3CMEDIUM POSITIONAL0.240.5
4DMEDIUM POSITIONAL0.170.5
1AMEDIUM THERMAL0.522
2BMEDIUM THERMAL0.532
3CMEDIUM THERMAL0.532
4DMEDIUM THERMAL0.512
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 427 -
Rwork0.203 8468 -
obs-8895 89.22 %

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