[English] 日本語
Yorodumi
- PDB-1amu: PHENYLALANINE ACTIVATING DOMAIN OF GRAMICIDIN SYNTHETASE 1 IN A C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1amu
TitlePHENYLALANINE ACTIVATING DOMAIN OF GRAMICIDIN SYNTHETASE 1 IN A COMPLEX WITH AMP AND PHENYLALANINE
ComponentsGRAMICIDIN SYNTHETASE 1
KeywordsPEPTIDE SYNTHETASE / GRSA / ADENYLATE FORMING
Function / homology
Function and homology information


phenylalanine racemase (ATP-hydrolysing) / phenylalanine racemase (ATP-hydrolyzing) activity / lipid biosynthetic process / ligase activity / antibiotic biosynthetic process / ATP binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / Non-ribosomal peptide synthase / ANL, C-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / Non-ribosomal peptide synthase / ANL, C-terminal domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHENYLALANINE / Gramicidin S synthase 1 / Gramicidin S synthase 1
Similarity search - Component
Biological speciesBrevibacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsConti, E. / Stachelhaus, T. / Marahiel, M.A. / Brick, P.
Citation
Journal: EMBO J. / Year: 1997
Title: Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S.
Authors: Conti, E. / Stachelhaus, T. / Marahiel, M.A. / Brick, P.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Modular Structure of Peptide Synthetases Revealed by Dissection of the Multifunctional Enzyme Grsa
Authors: Stachelhaus, T. / Marahiel, M.A.
History
DepositionJun 18, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_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.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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _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: GRAMICIDIN SYNTHETASE 1
B: GRAMICIDIN SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,52910
Polymers128,2642
Non-polymers1,2668
Water10,251569
1
A: GRAMICIDIN SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7655
Polymers64,1321
Non-polymers6334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GRAMICIDIN SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7655
Polymers64,1321
Non-polymers6334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.680, 154.770, 65.300
Angle α, β, γ (deg.)90.00, 93.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein GRAMICIDIN SYNTHETASE 1 / GRSA


Mass: 64131.793 Da / Num. of mol.: 2
Fragment: ADENYLATE FORMING DOMAIN, RESIDUES 1 - 556 PLUS A 7 RESIDUE C-TERMINAL TAG - SHHHHHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: GRSA / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(PREP4)
References: UniProt: P14687, UniProt: P0C061*PLUS, phenylalanine racemase (ATP-hydrolysing)

-
Non-polymers , 5 types, 577 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION TECHNIQUE. THE PROTEIN AT 15 MG/ML IN 10 MM TRIS-HCL PH7.8, 50 MM NACL, 15% GLYCEROL, 2 MM ATP, 2 MM L-PHE AND 4 MM MGCL2 WAS EQUILIBRATED WITH ...Details: CRYSTALS WERE GROWN USING THE VAPOR DIFFUSION TECHNIQUE. THE PROTEIN AT 15 MG/ML IN 10 MM TRIS-HCL PH7.8, 50 MM NACL, 15% GLYCEROL, 2 MM ATP, 2 MM L-PHE AND 4 MM MGCL2 WAS EQUILIBRATED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 28-32%(W/V) METHOXY POLYETHYLENE GLYCOL 5000, 200 MM AMMONIUM SULFATE, AND 100 MM ADA PH6.5 AT 18C., vapor diffusion, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNaCl
415 %glycerol1drop
52 mMATP1drop
62 mML-phenylalanine1drop
74 mM1dropMgCl2
828-32 %(w/v)MePEG50001reservoir
9200 mMammonium sulfate1reservoir
10100 mMADA1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.88
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 9, 1996
RadiationMonochromator: Y / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 91144 / % possible obs: 96.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 2.7 / % possible all: 88.3
Reflection
*PLUS
Num. measured all: 230285
Reflection shell
*PLUS
% possible obs: 88.3 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4SUITEdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3656 4 %RANDOM
Rwork0.213 ---
obs0.213 91142 95.3 %-
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7897 0 54 569 8520
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.37
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.331 437 3.31 %
Rwork0.331 9969 -
obs--87.12 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

+
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://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