[English] 日本語
Yorodumi
- PDB-1a9x: CARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a9x
TitleCARBAMOYL PHOSPHATE SYNTHETASE: CAUGHT IN THE ACT OF GLUTAMINE HYDROLYSIS
Components(CARBAMOYL PHOSPHATE SYNTHETASE ...) x 2
KeywordsAMIDOTRANSFERASE / THIOESTER
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 / cytosol / cytoplasm
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 / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / ATP-grasp fold, A domain / Class I glutamine amidotransferase (GATase) domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsThoden, J. / Holden, H.
CitationJournal: Biochemistry / Year: 1998
Title: Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis.
Authors: Thoden, J.B. / Miran, S.G. / Phillips, J.C. / Howard, A.J. / Raushel, F.M. / Holden, H.M.
History
DepositionApr 14, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)645,640111
Polymers636,8458
Non-polymers8,795103
Water81,5724528
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
B: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polymers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-77 kcal/mol
Surface area46650 Å2
MethodPISA, PQS
3
G: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
H: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polymers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-76 kcal/mol
Surface area46880 Å2
MethodPISA, PQS
4
C: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
D: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,43428
Polymers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-74 kcal/mol
Surface area46920 Å2
MethodPISA, PQS
5
E: CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)
F: CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,33927
Polymers159,2112
Non-polymers2,12725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-72 kcal/mol
Surface area46700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.100, 164.400, 332.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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

#1: Protein
CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)


Mass: 117956.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00968
#2: Protein
CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)


Mass: 41254.520 Da / Num. of mol.: 4 / Mutation: H353N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00907, UniProt: P0A6F1*PLUS

-
Non-polymers , 8 types, 4631 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


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


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


Mass: 35.453 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cl
#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.: 4528 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62 %
Crystal growpH: 7.4
Details: 0.65M NET4CL 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 THEN SOAKED INTO: 1.4M NET4CL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ...Details: 0.65M NET4CL 8% PEG 8000 100MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 THEN SOAKED INTO: 1.4M NET4CL 8% PEG 8000 250MM KCL 2.5MM MNCL2 2.5MM ADP 2.5MM ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 7.5% ETHYLENE GLYCOL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / pH: 8 / Method: batch method / Details: Thoden, J.B., (1995) Acta Crysta., D51, 827.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM11KCl
20.5 mML-ornithine11
30.5 mM11MnCl2
42.5 mMADP11
58 %PEG800011
60.65 Mtetraethylammonium chloride11
712.5 mMHEPPS11
82.5 mM11BeF3
95 mMglutamine11

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.2
DetectorType: BRUKER / Detector: CCD / Date: Nov 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 700998 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 23.8
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4 / Rsym value: 0.275 / % possible all: 91
Reflection
*PLUS
Num. measured all: 1676492
Reflection shell
*PLUS
% possible obs: 91 % / Num. unique obs: 85888 / Num. measured obs: 170785

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
SAINT2000data reduction
XCALIBREdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JDB

1jdb


Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.191 700998 -
obs-700998 92 %
Solvent computationSolvent model: TNT / Bsol: 290.8 Å2 / ksol: 0.99 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44248 0 435 4528 49211
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.014454676
X-RAY DIFFRACTIONt_angle_deg2.526130710
X-RAY DIFFRACTIONt_dihedral_angle_d17.7274210
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008122918
X-RAY DIFFRACTIONt_gen_planes0.01657950
X-RAY DIFFRACTIONt_it0493100
X-RAY DIFFRACTIONt_nbd0.032367
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.70
X-RAY DIFFRACTIONt_planar_d0.00818
X-RAY DIFFRACTIONt_plane_restr0.0150

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more