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- PDB-5ein: Crystal structure of C148A mutant of LysY from Thermus thermophil... -

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Basic information

Entry
Database: PDB / ID: 5ein
TitleCrystal structure of C148A mutant of LysY from Thermus thermophilus in complex with NADP+ and LysW-gamma-aminoadipic acid
Components
  • Alpha-aminoadipate carrier protein LysW
  • N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
KeywordsOXIDOREDUCTASE/BIOSYNTHETIC PROTEIN / amino group-carrier-protein / lysine biosynthesis / GAPDH family / OXIDOREDUCTASE-BIOSYNTHETIC PROTEIN complex
Function / homology
Function and homology information


[amino-group carrier protein]-6-phospho-L-2-aminoadipate reductase / N-acetyl-gamma-aminoadipyl-phosphate reductase activity / N-acetyl-gamma-glutamyl-phosphate reductase activity / L-lysine biosynthetic process via aminoadipic acid / L-arginine biosynthetic process / NADP+ binding / NAD binding / metal ion binding / cytoplasm
Similarity search - Function
[LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase / Lysine biosynthesis protein LysW / : / Alpha-aminoadipate carrier protein LysW-like, globular domain / : / N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / Semialdehyde dehydrogenase, dimerisation domain / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain ...[LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase / Lysine biosynthesis protein LysW / : / Alpha-aminoadipate carrier protein LysW-like, globular domain / : / N-acetyl-gamma-glutamyl-phosphate reductase, type 1 / N-acetyl-gamma-glutamyl-phosphate reductase, active site / Semialdehyde dehydrogenase, dimerisation domain / N-acetyl-gamma-glutamyl-phosphate reductase active site. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / TFIIB zinc-binding / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / [LysW]-L-2-aminoadipate 6-phosphate reductase / Alpha-aminoadipate carrier protein LysW
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShimizu, T. / Tomita, T. / Nishiyama, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure of the LysYLysW Complex from Thermus thermophilus.
Authors: Shimizu, T. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
History
DepositionOct 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Apr 5, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _refine.B_iso_mean / _refine.aniso_B[1][3] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_shell.d_res_low / _reflns.d_resolution_low / _reflns_shell.percent_possible_all / _struct_conn.conn_type_id / _struct_conn.id / _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_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_conn_type.id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
C: Alpha-aminoadipate carrier protein LysW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,71029
Polymers82,0993
Non-polymers2,61126
Water9,962553
1
A: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
C: Alpha-aminoadipate carrier protein LysW
hetero molecules

A: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
B: N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase
C: Alpha-aminoadipate carrier protein LysW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,41958
Polymers164,1986
Non-polymers5,22252
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Unit cell
Length a, b, c (Å)83.540, 83.540, 167.781
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase / AGPR / N-acetyl-glutamate semialdehyde/N-acetyl-aminoadipate semialdehyde dehydrogenase / NAGSA dehydrogenase


Mass: 38070.590 Da / Num. of mol.: 2 / Mutation: C148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: argC2, argC, lysY, TT_C1542 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus RIL
References: UniProt: O50146, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, N-acetyl-gamma-glutamyl-phosphate reductase
#2: Protein Alpha-aminoadipate carrier protein LysW


Mass: 5957.581 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: orfF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): CodonPlus RIL / References: UniProt: Q9ZND7

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Non-polymers , 4 types, 579 molecules

#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, magnesium formate, NADP+, HEPES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 8, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 75384 / % possible obs: 98.9 % / Redundancy: 5.5 % / Net I/σ(I): 38.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Cootmodel building
HKL-2000data scaling
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EIO

5eio


Resolution: 1.7→44.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.213 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3761 5 %RANDOM
Rwork0.171 ---
obs0.173 70757 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.66 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 166 553 6498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196104
X-RAY DIFFRACTIONr_bond_other_d0.0010.025781
X-RAY DIFFRACTIONr_angle_refined_deg1.49328288
X-RAY DIFFRACTIONr_angle_other_deg0.802313287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74222.462264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4515936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3521554
X-RAY DIFFRACTIONr_chiral_restr0.0870.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021420
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6912.7852964
X-RAY DIFFRACTIONr_mcbond_other1.6912.7862965
X-RAY DIFFRACTIONr_mcangle_it2.6654.1743702
X-RAY DIFFRACTIONr_mcangle_other2.6654.1743703
X-RAY DIFFRACTIONr_scbond_it1.973.0883140
X-RAY DIFFRACTIONr_scbond_other1.9513.0623092
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1044.5064586
X-RAY DIFFRACTIONr_long_range_B_refined5.39223.3267038
X-RAY DIFFRACTIONr_long_range_B_other5.39223.337039
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 280 -
Rwork0.231 5219 -
obs--100 %

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