[English] 日本語
Yorodumi
- PDB-1hop: STRUCTURE OF GUANINE NUCLEOTIDE (GPPCP) COMPLEX OF ADENYLOSUCCINA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hop
TitleSTRUCTURE OF GUANINE NUCLEOTIDE (GPPCP) COMPLEX OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI AT PH 6.5 AND 25 DEGREES CELSIUS
ComponentsADENYLOSUCCINATE SYNTHETASE
KeywordsLIGASE (SYNTHETASE) / PURINE NUCLEOTIDE BIOSYNTHESIS / LIGASE / GTP-BINDING ENZYMES / SYNTHETASE
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding ...adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding / magnesium ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 ...Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsPoland, B.W. / Hou, Z. / Bruns, C. / Fromm, H.J. / Honzatko, R.B.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli.
Authors: Poland, B.W. / Hou, Z. / Bruns, C. / Fromm, H.J. / Honzatko, R.B.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Refined Crystal Structures of Unligated Adenylosuccinate Synthetase from Escherichia Coli
Authors: Silva, M.M. / Poland, B.W. / Hoffman, C.R. / Fromm, H.J. / Honzatko, R.B.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Crystal Structure of Adenylosuccinate Synthetase from Escherichia Coli
Authors: Poland, B.W. / Silva, M.M. / Serra, M.A. / Cho, Y. / Kim, K.H. / Harris, E.M. / Honzatko, R.B.
History
DepositionApr 26, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ADENYLOSUCCINATE SYNTHETASE
B: ADENYLOSUCCINATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5824
Polymers94,5392
Non-polymers1,0422
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-22 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.850, 94.060, 119.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98924, 0.01055, -0.14595), (-0.03732, -0.98261, 0.18189), (-0.14149, 0.18538, 0.97243)
Vector: 31.99035, 89.31251, -5.93637)

-
Components

#1: Protein ADENYLOSUCCINATE SYNTHETASE


Mass: 47269.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NATIVE P212121 CRYSTALS WERE SOAKED WITH 5'-GUANOSYL-METHYLENE-TRIPHOSPHATE
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: H1238 / References: UniProt: P0A7D4, adenylosuccinate synthase
#2: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growpH: 6.5
Details: NATIVE P212121 CRYSTALS WERE SOAKED WITH 5'-GUANOSYL-METHYLENE-TRIPHOSPHATE., pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlenzyme1drop
220 mMimidazole1drop
375 mMsuccinate1drop
40.07 ml/L2-mercaptoethanol1drop
515 %(w/w)PEG33501drop
660 mMacetic acid1drop
7120 mMammonium sulfate1drop
825 %(w/w)PEG33501reservoir
9100 mMacetic acid1reservoir
10200 mMammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 37785 / % possible obs: 93 % / Redundancy: 2.09 % / Rmerge(I) obs: 0.082
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 78880
Reflection shell
*PLUS
% possible obs: 85 %

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.3→15 Å / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.227 --
Rwork0.19 --
obs0.19 28364 70 %
Displacement parametersBiso mean: 26.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8138 0 88 1035 9261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.19 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.75

+
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