[English] 日本語
Yorodumi
- PDB-1cdd: STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cdd
TitleSTRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
ComponentsPHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
KeywordsTRANSFERASE(FORMYL)
Function / homology
Function and homology information


phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / DNA damage response / cytoplasm / cytosol
Similarity search - Function
Phosphoribosylglycinamide formyltransferase / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsAlmassy, R.J. / Janson, C.A. / Kan, C.-C. / Hostomska, Z.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase.
Authors: Almassy, R.J. / Janson, C.A. / Kan, C.C. / Hostomska, Z.
#1: Journal: Nucleic Acids Res. / Year: 1990
Title: De Novo Purine Nucleotide Biosynthesis: Cloning of Human and Avian Cdna'S Encoding the Trifunctional Glycinamide Ribonucleotide Synthetase-Aminoimidazole Ribonucleotide Synthetase-Glycinamide ...Title: De Novo Purine Nucleotide Biosynthesis: Cloning of Human and Avian Cdna'S Encoding the Trifunctional Glycinamide Ribonucleotide Synthetase-Aminoimidazole Ribonucleotide Synthetase-Glycinamide Ribonucleotide Transformylase by Functional Complementation in E. Coli
Authors: Aimi, J. / Qiu, H. / Williams, J. / Zalkin, H. / Dixon, J.E.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: Identification and Nucleotide Sequence of a Gene Encoding 5'-Phosphoribosylglycinamide Transformylase in Escherichia Coli K12
Authors: Smith, J.M. / Daum III, H.A.
History
DepositionMay 15, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
B: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7224
Polymers46,5332
Non-polymers1902
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-23 kcal/mol
Surface area17790 Å2
MethodPISA
2
A: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules

B: PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7224
Polymers46,5332
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645-x+3/2,y-1/2,-z+1/21
Buried area2280 Å2
ΔGint-26 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.900, 97.600, 102.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: PRO B 204 - PRO B 205 OMEGA =212.30 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.19391, 0.33875, 0.92068), (0.43494, -0.81152, 0.3902), (0.87933, 0.47611, 0.01002)
Vector: 112.79, 1.83, -101.45)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR MOLECULE 1 (CHAIN A) WHEN APPLIED TO MOLECULE 2 (CHAIN B) WITH AN RMS DEVIATION OF 0.83 ANGSTROMS FOR 189 CA COORDINATES (APPROXIMATELY A TWO-FOLD ROTATION, 184 DEGREES).

-
Components

#1: Protein PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE


Mass: 23266.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain (production host): K12
References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.47 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
250 mMTris1drop
31 mMdithiothreitol1drop
40.8 MNa+/K+ phosphate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Num. all: 124304 / Num. obs: 16623 / Rmerge(I) obs: 0.074

-
Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.225 / Highest resolution: 2.8 Å
Details: RESIDUES 210 - 212 IN CHAIN A HAVE HIGH TEMPERATURE FACTORS, ARE IN WEAK DENSITY, AND HAVE SIGNIFICANT DISORDER.
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 10 0 2918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d4.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 15431 / σ(F): 0.5 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg4.1

+
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://pdbjlvh1.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