[English] 日本語
Yorodumi
- PDB-1z7e: Crystal structure of full length ArnA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z7e
TitleCrystal structure of full length ArnA
Componentsprotein ArnA
KeywordsHYDROLASE / Rossmann fold / OB-like fold
Function / homology
Function and homology information


UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding ...UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding / response to antibiotic / protein-containing complex / identical protein binding
Similarity search - Function
Rossmann fold - #12230 / Bifunctional polymyxin resistance protein, ArnA / Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / NAD-dependent epimerase/dehydratase ...Rossmann fold - #12230 / Bifunctional polymyxin resistance protein, ArnA / Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / Bifunctional polymyxin resistance protein ArnA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGatzeva-Topalova, P.Z. / May, A.P. / Sousa, M.C.
CitationJournal: Structure / Year: 2005
Title: Structure and Mechanism of ArnA: Conformational Change Implies Ordered Dehydrogenase Mechanism in Key Enzyme for Polymyxin Resistance
Authors: Gatzeva-Topalova, P.Z. / May, A.P. / Sousa, M.C.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: protein ArnA
B: protein ArnA
C: protein ArnA
D: protein ArnA
E: protein ArnA
F: protein ArnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,83918
Polymers446,3156
Non-polymers6,52512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33970 Å2
ΔGint-146 kcal/mol
Surface area145130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.689, 166.227, 261.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Protein
protein ArnA / Hypothetical protein yfbG


Mass: 74385.773 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: full length / Source: (gene. exp.) Escherichia coli (E. coli) / Description: plasmid is AN ENGINEERED VARIANT OF THE PET28 / Gene: PMRI, YFBG / Plasmid: PMS122 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: P77398
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H22N2O18P2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M MES pH 7.0, 10% Ethylene glycol, 9% PEG 8000, 14 mM 2mercaptoethanol and 10 mM ATP; protein was pre-incubated on ice with 3mM UDP-GlcA and 3 mM MgSO4 , VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1808 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 132644 / Num. obs: 131520 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.9 / Num. unique all: 13215 / % possible all: 99.8

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U9J, 1YRW

1u9j

1yrw


Resolution: 3→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 135954.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 12667 10 %RANDOM
Rwork0.225 ---
all0.2251 132762 --
obs0.2251 126417 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.7321 Å2 / ksol: 0.390853 e/Å3
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å20 Å2
2---12.76 Å20 Å2
3---14.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30148 0 408 0 30556
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 1169 9.9 %
Rwork0.317 10626 -
obs-11795 89.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMATP_UGA_REV.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4ATP_UGA_REV.PARAM

+
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