[English] 日本語
Yorodumi
- PDB-1ce8: CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIS COLI WITH COMPLEX... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1ce8
TitleCARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIS COLI WITH COMPLEXED WITH THE ALLOSTERIC LIGAND IMP
Components(PROTEIN (CARBAMOYL-PHOSPHATE ...) x 2
KeywordsLIGASE IMP / IMP / ALLOSTERIC LIGAND
Function / homologyCarbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / ATP-grasp fold / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase, large subunit / Class I glutamine amidotransferase-like / 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, small subunit / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / ATP-grasp fold / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase, large subunit / Class I glutamine amidotransferase-like / 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 large chain / Carbamoyl-phosphate synthase small chain
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.1 Å resolution
AuthorsThoden, J.B. / Raushel, F.M. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase.
Authors: Thoden, J.B. / Raushel, F.M. / Wesenberg, G. / Holden, H.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 18, 1999 / Release: Jul 26, 1999
RevisionDateData content typeGroupProviderType
1.0Jul 26, 1999Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
B: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
C: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
D: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
E: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
F: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
G: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
H: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)646,80288
Polyers637,8548
Non-polymers8,94880
Water72,7274037
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
B: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70122
Polyers159,4642
Non-polymers2,23720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8520
ΔGint (kcal/M)-60
Surface area (Å2)46890
MethodPISA,PQS
3
G: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
H: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70122
Polyers159,4642
Non-polymers2,23720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8480
ΔGint (kcal/M)-60
Surface area (Å2)46830
MethodPISA,PQS
4
C: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
D: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70122
Polyers159,4642
Non-polymers2,23720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8340
ΔGint (kcal/M)-57
Surface area (Å2)47010
MethodPISA,PQS
5
E: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
F: PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,70122
Polyers159,4642
Non-polymers2,23720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8500
ΔGint (kcal/M)-55
Surface area (Å2)46570
MethodPISA,PQS
Unit cell
γ
α
β
Length a, b, c (Å)152.100, 163.900, 331.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

-
Components

-
PROTEIN (CARBAMOYL-PHOSPHATE ... , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)


Mass: 117982.688 Da / Num. of mol.: 4 / Details: LONG CHAIN / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli)
References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing)
#2: Protein/peptide
PROTEIN (CARBAMOYL-PHOSPHATE SYNTHASE)


Mass: 41480.895 Da / Num. of mol.: 4 / Details: SHORT CHAIN / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6F1, carbamoyl-phosphate synthase (glutamine-hydrolysing)

-
Non-polymers , 9 types, 4117 molecules

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


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


Mass: 39.098 Da / Num. of mol.: 28 / Formula: K / Potassium
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Formula: Cl / Chloride
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Formula: PO4 / Phosphate
#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.: 8 / Formula: C5H12N2O2 / Ornithine
#9: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Formula: C10H13N4O8P / Inosinic acid
#10: Chemical
ChemComp-NET / TETRAETHYLAMMONIUM ION


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


Mass: 18.015 Da / Num. of mol.: 4037 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 / Density percent sol: 62 %
Crystal growpH: 7.4 / Details: pH 7.4
Crystal grow
*PLUS
Temp: 4 ℃ / Method: unknown
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
10.65 Mtetraethylammonium chloride11
28 %(w/v)PEG800011
3100 mM11KCl
40.5 mM11MnCl2
50.5 mMornithine11
61.25 mMADP11
71.25 mMBeF311
85.0 mMIMP11
925 mMHEPES11

-
Data collection

DiffractionMean temperature: 130 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL7-1 / Synchrotron site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Feb 1, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionD resolution high: 2.1 Å / D resolution low: 3 Å / Number obs: 445013 / Observed criterion sigma I: 0 / Rmerge I obs: 0.05 / Rsym value: 0.05 / NetI over sigmaI: 30.3 / Redundancy: 4 % / Percent possible obs: 93
Reflection shellRmerge I obs: 0.221 / Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / MeanI over sigI obs: 3.9 / Rsym value: 0.221 / Redundancy: 2.3 % / Percent possible all: 81
Reflection shell
*PLUS
Number unique obs: 38417 / Percent possible obs: 81

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5Drefinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A9X
Details: MISSING RESIDUES THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP THR: LAST TWO RESIDUES, 381ALA AND 382LYS ARE NOT VISIBLE IN ELECTRON DENSITY MAP
R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: TNT PROTGEO
Solvent computationSolvent model details: TNT / Solvent model param bsol: 403.8 / Solvent model param ksol: 0.881
Least-squares processR factor R free: 0.25 / R factor R work: 0.193 / R factor all: 0.193 / R factor obs: 0.192 / Highest resolution: 2.1 Å / Lowest resolution: 3 Å / Number reflection R free: 2225 / Number reflection all: 445013 / Number reflection obs: 445013 / Percent reflection R free: 5 / Percent reflection obs: 93
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 44220 / Nucleic acid: 0 / Ligand: 488 / Solvent: 4037 / Total: 48745
Refine LS restraints
Refine IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.013455637.500
X-RAY DIFFRACTIONt_angle_deg2.3006144613.000
X-RAY DIFFRACTIONt_dihedral_angle_d17.899274560.000
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005122440.000
X-RAY DIFFRACTIONt_gen_planes0.009660565.000
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.040796
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Least-squares process
*PLUS
R factor R free: 0.257 / R factor R work: 0.193 / R factor all: 0.192 / Number reflection R free: 22250
Refine LS restraints
*PLUS
Refine IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.8990.000
X-RAY DIFFRACTIONt_planar_d0.00540.000
X-RAY DIFFRACTIONt_plane_restr0.00965.000

+
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