[English] 日本語
Yorodumi
- PDB-1t36: Crystal structure of E. coli carbamoyl phosphate synthetase small... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t36
TitleCrystal structure of E. coli carbamoyl phosphate synthetase small subunit mutant C248D complexed with uridine 5'-monophosphate
Components(Carbamoyl-phosphate synthase ...) x 2
KeywordsLIGASE / channeling / pyrimidine biosynthesis / arginine biosynthesis
Function / homology
Function and homology information


carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / arginine biosynthetic process / glutamine metabolic process / amino acid binding / cellular amino acid biosynthetic process / nitrogen compound metabolic process ...carbamoyl-phosphate synthase complex / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / pyrimidine nucleobase biosynthetic process / arginine biosynthetic process / glutamine metabolic process / amino acid binding / cellular amino acid biosynthetic process / nitrogen compound metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleotide binding / ATP binding / metal ion binding / cytosol / cytoplasm
Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Pre-ATP-grasp domain superfamily / ATP-grasp fold / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase, large subunit / 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, GATase1 domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Pre-ATP-grasp domain superfamily / ATP-grasp fold / Methylglyoxal synthase-like domain / Carbamoyl-phosphate synthase, large subunit / 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, N-terminal domain superfamily / Methylglyoxal synthase-like domain superfamily / Class I glutamine amidotransferase-like / MGS-like domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Glutamine amidotransferase class-I / Carbamoyl-phosphate synthase small chain, CPSase domain / Glutamine amidotransferase / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl Phosphate Synthetase; Chain A, domain 4 / Methylglyoxal synthase-like domain / Glucose Oxidase; domain 1 / Rossmann fold - #20 / ATP-grasp fold, A domain / Class I glutamine amidotransferase (GATase) domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / 3-Layer(bba) Sandwich / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Carbamoyl-phosphate synthase small chain / Carbamoyl-phosphate synthase large chain / Carbamoyl-phosphate synthase small chain
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsThoden, J.B. / Huang, X. / Raushel, F.M. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2004
Title: Long-range allosteric transitions in carbamoyl phosphate synthetase.
Authors: Thoden, J.B. / Huang, X. / Kim, J. / Raushel, F.M. / Holden, H.M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbamoyl-phosphate synthase large chain
B: Carbamoyl-phosphate synthase small chain
C: Carbamoyl-phosphate synthase large chain
D: Carbamoyl-phosphate synthase small chain
E: Carbamoyl-phosphate synthase large chain
F: Carbamoyl-phosphate synthase small chain
G: Carbamoyl-phosphate synthase large chain
H: Carbamoyl-phosphate synthase small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)646,61894
Polymers637,9028
Non-polymers8,71586
Water70,3853907
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)152.500, 164.900, 333.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsHetero-octamer comprising chains A,B,C,D,E,F,G,H. THese chains, as deposited, represent the biological assebmly

-
Components

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

#1: Protein
Carbamoyl-phosphate synthase 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, PYRA, B0033 / Plasmid: pet15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P00968, carbamoyl-phosphate synthase (glutamine-hydrolysing)
#2: Protein
Carbamoyl-phosphate synthase small chain / Carbamoyl-phosphate synthetase glutamine chain


Mass: 41493.824 Da / Num. of mol.: 4 / Mutation: C248D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CARA, PYRA, B0032, Z0037, ECS0035 / Plasmid: pet15 / Production host: Escherichia coli (E. coli)
References: UniProt: P00907, UniProt: P0A6F1*PLUS, carbamoyl-phosphate synthase (glutamine-hydrolysing)

-
Non-polymers , 9 types, 3993 molecules

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


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


Mass: 39.098 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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 / Ornithine


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


Mass: 130.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H20N
#10: Chemical
ChemComp-U / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3907 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 277 K / Method: batch / pH: 7.4
Details: PEG 8000, tetramethylammonium chloride, potassium chloride, manganese chloride, ornithine, ADP, HEPES, pH 7.4, batch, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.65 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 433843 / Num. obs: 433843 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.048 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 39976 / Rsym value: 0.203 / % possible all: 83

-
Processing

Software
NameClassification
d*TREKdata scaling
SCALEPACKdata scaling
TNTrefinement
d*TREKdata reduction
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1JDB

1jdb


Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 42551 -randon
Rwork0.176 ---
Obs0.179 433843 90 %-
All-433843 --
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44228 0 458 3907 48593
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.43

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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. (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 PDBe / 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

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