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- PDB-1kee: Inactivation of the Amidotransferase Activity of Carbamoyl Phosph... -

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Basic information

Entry
Database: PDB / ID: 1kee
TitleInactivation of the Amidotransferase Activity of Carbamoyl Phosphate Synthetase by the Antibiotic Acivicin
Components(Carbamoyl-phosphate synthetase ...) x 2
KeywordsLIGASE / ATP grasp / channeling / antibiotic
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / : / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / glutaminase activity / L-arginine biosynthetic process / glutamine metabolic process ...carbamoyl-phosphate synthase complex / : / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / glutaminase activity / L-arginine biosynthetic process / glutamine metabolic process / amino acid binding / amino acid biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein heterodimerization activity / nucleotide binding / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like domain / Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / : / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit ...Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like domain / Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / : / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Glucose Oxidase; domain 1 / Rossmann fold - #20 / Glutamine amidotransferase / Glutamine amidotransferase class-I / Carbamoyl-phosphate synthase subdomain signature 1. / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, A domain / Class I glutamine amidotransferase (GATase) domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 3-Layer(bba) Sandwich / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / : / TETRAETHYLAMMONIUM ION / L-ornithine / PHOSPHATE ION / Carbamoyl-phosphate synthase small chain / Carbamoyl phosphate synthase large chain / Carbamoyl phosphate synthase small chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsMiles, B.W. / Thoden, J.B. / Holden, H.M. / Raushel, F.M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Inactivation of the amidotransferase activity of carbamoyl phosphate synthetase by the antibiotic acivicin.
Authors: Miles, B.W. / Thoden, J.B. / Holden, H.M. / Raushel, F.M.
History
DepositionNov 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / software / struct_conn / struct_ref_seq_dif
Item: _software.classification / _software.name / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: 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_conn_type / 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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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: Carbamoyl-phosphate synthetase large chain
B: Carbamoyl-phosphate synthetase small chain
C: Carbamoyl-phosphate synthetase large chain
D: Carbamoyl-phosphate synthetase small chain
E: Carbamoyl-phosphate synthetase large chain
F: Carbamoyl-phosphate synthetase small chain
G: Carbamoyl-phosphate synthetase large chain
H: Carbamoyl-phosphate synthetase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,96094
Polymers638,4238
Non-polymers7,53786
Water75,2314176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Carbamoyl-phosphate synthetase large chain
H: Carbamoyl-phosphate synthetase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,47223
Polymers159,6062
Non-polymers1,86721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-55 kcal/mol
Surface area46990 Å2
MethodPISA, PQS
3
E: Carbamoyl-phosphate synthetase large chain
F: Carbamoyl-phosphate synthetase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,47223
Polymers159,6062
Non-polymers1,86721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-53 kcal/mol
Surface area46910 Å2
MethodPISA, PQS
4
A: Carbamoyl-phosphate synthetase large chain
B: Carbamoyl-phosphate synthetase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,50824
Polymers159,6062
Non-polymers1,90222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-58 kcal/mol
Surface area46970 Å2
MethodPISA, PQS
5
C: Carbamoyl-phosphate synthetase large chain
D: Carbamoyl-phosphate synthetase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,50824
Polymers159,6062
Non-polymers1,90222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-63 kcal/mol
Surface area47070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.400, 164.400, 333.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is an octamer comprised of chains A,B,C,D,E,F,G, and H

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Components

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Carbamoyl-phosphate synthetase ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Carbamoyl-phosphate synthetase large chain / CARBAMOYL-PHOSPHATE SYNTHETASE AMMONIA CHAIN


Mass: 117981.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CARB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3(pLysS)
References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing)
#2: Protein
Carbamoyl-phosphate synthetase small chain / CARBAMOYL-PHOSPHATE SYNTHETASE GLUTAMINE CHAIN


Mass: 41623.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CARA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3(PysS)lysS)
References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing)

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Non-polymers , 8 types, 4262 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#4: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: K
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#8: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2
#9: Chemical
ChemComp-NET / TETRAETHYLAMMONIUM ION


Mass: 130.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H20N
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4176 / 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: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 277 K / Method: batch / pH: 7.4
Details: PEG 8000, Hepes, potassium chloride, manganese chloride, ornithine, tetraethylammonium chloride, HEPPS, pH 7.4, batch, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein11
210 mMHEPES11pH7.0
3100 mM11KCl
40.65 Mtetraethylammonium chloride12
58 %(w/v)PEG800012
6100 mM12KCl
70.5 mM12MnCl2
80.5 mMornithine12
91.25 mMADP12
1025 mMHEPES12pH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.908 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 429957 / Num. obs: 429957 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 37.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 5.9 / Num. unique all: 34861 / Rsym value: 0.179 / % possible all: 72.7
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 72.7 % / Num. unique obs: 34861

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Processing

Software
NameClassification
TNTrefinement
MAR345data collection
SCALEPACKdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1JDB

1jdb


Resolution: 2.1→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 42997 -RANDOM
Rwork0.186 ---
all0.187 429957 --
obs0.187 429957 88.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44260 0 374 4176 48810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.12
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_dihedral_angle_d17.7
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.187 / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.12
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.7
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.01

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