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- PDB-1c30: CRYSTAL STRUCTURE OF CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNI... -

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Basic information

Entry
Database: PDB / ID: 1c30
TitleCRYSTAL STRUCTURE OF CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT MUTATION C269S
Components(CARBAMOYL PHOSPHATE SYNTHETASE: ...) x 2
KeywordsLIGASE / AMIDOTRANSFERASE / ATP-GRASP / SUBSTRATE CHANNELING
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / : / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / L-arginine biosynthetic process / glutaminase activity / amino acid binding ...carbamoyl-phosphate synthase complex / : / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / L-arginine biosynthetic process / glutaminase activity / amino acid binding / glutamine metabolic process / 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 / cytosol / cytoplasm
Similarity search - Function
Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like 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 Synthetase; Chain A, domain 4 / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like 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 / Glutamine amidotransferase / Glutamine amidotransferase class-I / Rossmann fold - #20 / Glucose Oxidase; domain 1 / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / 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 / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Class I glutamine amidotransferase-like / 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 / Resolution: 2 Å
AuthorsThoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1999
Title: The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway.
Authors: Thoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M.
History
DepositionJul 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_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 SUBUNIT
B: CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT
C: CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT
D: CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT
E: CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT
F: CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT
G: CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT
H: CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,30590
Polymers637,7908
Non-polymers7,51582
Water71,8263987
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT
H: CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,14721
Polymers159,4482
Non-polymers1,69919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-62 kcal/mol
Surface area46830 Å2
MethodPISA, PQS
3
A: CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT
B: CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,67525
Polymers159,4482
Non-polymers2,22823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-62 kcal/mol
Surface area47500 Å2
MethodPISA, PQS
4
C: CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT
D: CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,24222
Polymers159,4482
Non-polymers1,79420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-64 kcal/mol
Surface area47000 Å2
MethodPISA, PQS
5
E: CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT
F: CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,24222
Polymers159,4482
Non-polymers1,79420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-64 kcal/mol
Surface area46640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.600, 164.600, 332.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CARBAMOYL PHOSPHATE SYNTHETASE: ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
CARBAMOYL PHOSPHATE SYNTHETASE: LARGE SUBUNIT


Mass: 117981.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Bacteria (eubacteria)
References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing)
#2: Protein
CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT


Mass: 41465.816 Da / Num. of mol.: 4 / Mutation: C269S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Bacteria (eubacteria)
References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing)

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Non-polymers , 8 types, 4069 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.: 16 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2
#8: 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
#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.: 3987 / 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: 62.43 %
Crystal growTemperature: 277 K / Method: batch / pH: 7.4
Details: PEG 8000, POTASSIUM CHLORIDE, MANGANESE CHLORIDE, TETRAETHYLAMMONIUM CHLORIDE, L-ORNITHINE, ADP, BERYLLIUM FLUORIDE, HEPPS, pH 7.4, BATCH, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 %PEG800011
20.65 Mtetraethylammonium chloride11
30.5 mM11MnCl2
4100 mM11KCl
51.5 mMADP11
61.5 mM11BeF3
70.5 mML-ornithine11
825 mMHEPPS11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.70849
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70849 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 546635 / Num. obs: 546635 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.291 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 2305540
Reflection shell
*PLUS
% possible obs: 96.8 % / Num. unique obs: 53813 / Num. measured obs: 186320 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
d*TREKdata reduction
HKL-2000data scaling
RefinementResolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.246 54664 -RANDOM
Rwork0.189 ---
all0.189 546635 --
obs0.189 546635 97.7 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44220 0 376 3987 48583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.26
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor all: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.26
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.011

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