[English] 日本語
Yorodumi
- PDB-1ecc: ESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ecc
TitleESCHERICHIA COLI GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE (PRPP) AMIDOTRANSFERASE COMPLEXED WITH MN-CPRPP AND 5-OXO-NORLEUCINE
ComponentsGLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
KeywordsTRANSFERASE / GLUTAMINE AMIDOTRANSFERASE / PURINE BIOSYNTHESIS / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / glutamine metabolic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glycosyltransferase activity / magnesium ion binding / identical protein binding ...amidophosphoribosyltransferase / amidophosphoribosyltransferase activity / purine nucleobase biosynthetic process / glutamine metabolic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / glycosyltransferase activity / magnesium ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain ...Amidophosphoribosyltransferase / Amidophosphoribosyltransferase, N-terminal / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 5-OXO-L-NORLEUCINE / Chem-PCP / Amidophosphoribosyltransferase / Amidophosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKrahn, J.M. / Smith, J.L.
CitationJournal: Biochemistry / Year: 1997
Title: Coupled formation of an amidotransferase interdomain ammonia channel and a phosphoribosyltransferase active site.
Authors: Krahn, J.M. / Kim, J.H. / Burns, M.R. / Parry, R.J. / Zalkin, H. / Smith, J.L.
History
DepositionJul 9, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
B: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,18711
Polymers112,8452
Non-polymers1,3419
Water5,242291
1
A: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
B: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules

A: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
B: GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,37322
Polymers225,6914
Non-polymers2,68218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)78.200, 78.200, 308.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.142832, 0.84025, 0.523047), (0.856486, -0.15991, 0.490775), (0.496014, 0.518081, -0.696822)
Vector: 44.385, -100.045, 92.628)

-
Components

#1: Protein GLUTAMINE PHOSPHORIBOSYLPYROPHOSPHATE AMIDOTRANSFERASE


Mass: 56422.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURF / Plasmid: PT7F1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P00496, UniProt: P0AG16*PLUS, amidophosphoribosyltransferase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ONL / 5-OXO-L-NORLEUCINE


Type: L-peptide linking / Mass: 145.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO3
#4: Chemical ChemComp-PCP / 1-ALPHA-PYROPHOSPHORYL-2-ALPHA,3-ALPHA-DIHYDROXY-4-BETA-CYCLOPENTANE-METHANOL-5-PHOSPHATE / CARBOXYLIC PRPP / CPRPP


Mass: 388.097 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O13P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsA WELL ORDERED MN++ EXISTS AT A LATTICE CONTACT. THIS METAL IS LIGATED TO GLU B 449, ASP B 471, AND ...A WELL ORDERED MN++ EXISTS AT A LATTICE CONTACT. THIS METAL IS LIGATED TO GLU B 449, ASP B 471, AND WATERS HOH A 507, HOH A 508, HOH B 507, AND HOH B 508. LIGATION TO ASP B 471 IS TO A SYMMETRY-EQUIVALENT RESIDUE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46 %
Description: A SINGLE GAT DOMAIN (249 RESIDUES) WAS USED AS THE PROBE MODEL DUE TO ALLOSTERIC DIFFERENCES BETWEEN THIS STRUCTURE AND THAT OF 1ECF.
Crystal growpH: 5.8
Details: 0.42MM CPRPP, 25MM MNCL2, 40MM BIS-TRIS PH 5.8, 3.2% 2-PROPANOL, 7.5% PEG-3350
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.6 mg/mlprotein1drop
20.42 mMcPRPP1drop
320 mM1dropMnCl2
440 mMBis-Tris1drop
53.2 %2-propanol1drop
67.5 %PEG33501drop
7100 mMbis-Tris1reservoir
88 %2-propanol1reservoir
915 %PEG33501reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1996
RadiationMonochromator: MSC DOUBLE MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 27331 / % possible obs: 88.3 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 42.9 Å2 / Rsym value: 0.036 / Net I/σ(I): 22.7
Reflection shellResolution: 2.4→2.5 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.172 / % possible all: 60.3
Reflection
*PLUS
Num. measured all: 99285 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 60.3 % / Rmerge(I) obs: 0.172

-
Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
HKL(DENZO)data reduction
HKLdata scaling
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ECF

1ecf


Resolution: 2.4→25 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: FREE R / σ(F): 0
Details: ADDITIONAL TOPOLOGY/PARAMETER FILES FOR THE CYS/ONL LINKAGE WERE USED, WHICH HAVE A NOMENCLATURE DIFFERENT FROM THE ONL RESIDUE IN THIS ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1679 5 %RANDOM, FROM ENTIRE DATA SET
Rwork0.176 ---
obs0.176 35343 88.3 %-
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.92 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7732 0 69 291 8092
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.97
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.574
X-RAY DIFFRACTIONx_mcangle_it22.636
X-RAY DIFFRACTIONx_scbond_it22.42
X-RAY DIFFRACTIONx_scangle_it2.53.78
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 127 5 %
Rwork0.295 2517 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11X.DNATOPH11.DNA
X-RAY DIFFRACTION3PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION4PRPP.PARCPRPP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47
LS refinement shell
*PLUS
Rfactor Rfree: 0.35

+
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