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

+
Open data


ID or keywords:

Loading...

no data

-
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 / homologyCarbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / ATP-grasp fold / Methylglyoxal synthase-like domain / Class I glutamine amidotransferase-like / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain ...Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / ATP-grasp fold / Methylglyoxal synthase-like domain / Class I glutamine amidotransferase-like / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthase large chain, methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Pre-ATP-grasp domain superfamily / Glutamine amidotransferase / Methylglyoxal synthase-like domain superfamily / Glutamine amidotransferase class-I / Carbamoyl-phosphate synthase small chain, CPSase domain / MGS-like domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthase subdomain signature 2. / ATP-grasp fold profile. / Glutamine amidotransferase type 1 domain profile. / MGS-like domain profile. / carbamoyl-phosphate synthase complex / pyrimidine nucleobase biosynthetic process / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl phosphate biosynthetic process / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / urea cycle / arginine biosynthetic process / glutamine metabolic process / cellular amino acid biosynthetic process / 'de novo' UMP biosynthetic process / amino acid binding / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to amino acid stimulus / nucleotide binding / ATP binding / metal ion binding / cytosol / cytoplasm / Carbamoyl-phosphate synthase small chain / Carbamoyl-phosphate synthase large chain / Carbamoyl-phosphate synthase small chain
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.8 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 14, 1998 / Release: Oct 21, 1998
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 21, 1998Structure modelrepositoryInitial release
1.1Mar 10, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance
1.3Mar 14, 2018Structure modelDatabase referencesstruct_ref_seq_dif_struct_ref_seq_dif.details

-
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
Polyers636,8458
Non-polymers8,795103
Water81,5724528
1


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
Polyers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8760
ΔGint (kcal/M)-77
Surface area (Å2)46650
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
Polyers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8710
ΔGint (kcal/M)-76
Surface area (Å2)46880
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
Polyers159,2112
Non-polymers2,22226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8740
ΔGint (kcal/M)-74
Surface area (Å2)46920
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
Polyers159,2112
Non-polymers2,12725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8640
ΔGint (kcal/M)-72
Surface area (Å2)46700
MethodPISA,PQS
Unit cell
γ
α
β
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-MP 21 21 21

-
Components

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

#1: Protein/peptide
CARBAMOYL PHOSPHATE SYNTHETASE (LARGE CHAIN)


Mass: 117956.656 Da / Num. of mol.: 4 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P00968
#2: Protein/peptide
CARBAMOYL PHOSPHATE SYNTHETASE (SMALL CHAIN)


Mass: 41254.520 Da / Num. of mol.: 4 / Mutation: H353N / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / 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 / Formula: PO4 / Phosphate
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


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


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


Mass: 35.453 Da / Num. of mol.: 28 / Formula: Cl / Chloride
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#8: Chemical
ChemComp-ORN / L-ornithine


Mass: 132.161 Da / Num. of mol.: 4 / Formula: C5H12N2O2 / Ornithine
#9: Chemical
ChemComp-NET / TETRAETHYLAMMONIUM ION


Mass: 130.251 Da / Num. of mol.: 4 / Formula: C8H20N / Tetraethylammonium
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4528 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.25 / Density percent 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 ORNITHINE 5MM GLUTAMINE 25MM HEPES PH 7.4 7.5% ETHYLENE GLYCOL
Crystal grow
*PLUS
Temp: 277 K / pH: 8 / Method: batch method / Details: Thoden, J.B., (1995) Acta Crysta., D51, 827.
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 17-ID / Synchrotron site: APS / Beamline: 17-ID / Wavelength: 1.2
DetectorType: BRUKER / Detector: CCD / Collection date: Nov 1, 1997
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / D resolution low: 30 Å / Number obs: 700998 / Observed criterion sigma I: 0 / Rmerge I obs: 0.065 / Rsym value: 0.065 / NetI over sigmaI: 23.8 / Redundancy: 2.4 % / Percent possible obs: 92
Reflection shellRmerge I obs: 0.275 / Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / MeanI over sigI obs: 4 / Rsym value: 0.275 / Redundancy: 2 % / Percent possible all: 91
Reflection
*PLUS
Number measured all: 1676492
Reflection shell
*PLUS
Number unique obs: 85888 / Number measured obs: 170785 / Percent possible obs: 91

-
Processing

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

1jdb


Sigma F: 0 / Stereochemistry target values: TNT PROTGEO
Solvent computationSolvent model details: TNT / Solvent model param bsol: 290.8 / Solvent model param ksol: 0.99
Least-squares processR factor all: 0.191 / Highest resolution: 1.8 Å / Lowest resolution: 3 Å / Number reflection all: 700998 / Number reflection obs: 700998 / Percent reflection obs: 92
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 44248 / Nucleic acid: 0 / Ligand: 435 / Solvent: 4528 / Total: 49211
Refine LS restraints
Refine IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.014454676.000
X-RAY DIFFRACTIONt_angle_deg2.526130710.000
X-RAY DIFFRACTIONt_dihedral_angle_d17.7274210.000
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008122918.000
X-RAY DIFFRACTIONt_gen_planes0.01657950.000
X-RAY DIFFRACTIONt_it0493100.0
X-RAY DIFFRACTIONt_nbd0.032367
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.70.000
X-RAY DIFFRACTIONt_planar_d0.00818.000
X-RAY DIFFRACTIONt_plane_restr0.0150.000

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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