[English] 日本語
Yorodumi
- PDB-6he2: Crystal structure of an open conformation of 2-Hydroxyisobutyryl-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6he2
TitleCrystal structure of an open conformation of 2-Hydroxyisobutyryl-CoA Ligase (HCL) in complex with 2-HIB-AMP and CoA
Components2-hydroxyisobutyryl-CoA synthetase
KeywordsLIGASE / 2-hydroxyisobutyrate CoA
Function / homology
Function and homology information


Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / ligase activity / nucleotide binding
Similarity search - Function
AMP-dependent ligase, C-terminal / AMP-binding enzyme C-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8LE / ADENOSINE MONOPHOSPHATE / COENZYME A / 2-hydroxyisobutyryl-CoA synthetase
Similarity search - Component
Biological speciesAquincola tertiaricarbonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZahn, M. / Rohwerder, T. / Strater, N.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structures of 2-Hydroxyisobutyric Acid-CoA Ligase Reveal Determinants of Substrate Specificity and Describe a Multi-Conformational Catalytic Cycle.
Authors: Zahn, M. / Kurteva-Yaneva, N. / Schuster, J. / Krug, U. / Georgi, T. / Muller, R.H. / Rohwerder, T. / Strater, N.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-hydroxyisobutyryl-CoA synthetase
B: 2-hydroxyisobutyryl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9828
Polymers111,8862
Non-polymers3,0966
Water5,242291
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-39 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.852, 101.847, 109.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 2-hydroxyisobutyryl-CoA synthetase


Mass: 55943.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquincola tertiaricarbonis (bacteria) / Gene: hcl / Production host: Escherichia coli (E. coli)
References: UniProt: I3VE75, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-8LE / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 2-methyl-2-oxidanyl-propanoate


Mass: 433.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N5O9P
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M TRIS PH 8.0, 24% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 47279 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 45.74 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 6830 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTER2.10.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y4O

2y4o


Resolution: 2.3→39.72 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.287 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.203
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1467 3.11 %RANDOM
Rwork0.184 ---
obs0.186 47200 99.8 %-
Displacement parametersBiso mean: 43.31 Å2
Baniso -1Baniso -2Baniso -3
1--13.0457 Å20 Å20 Å2
2--6.72 Å20 Å2
3---6.3257 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 200 291 7501
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097414HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0210091HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2531SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes163HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1141HARMONIC5
X-RAY DIFFRACTIONt_it7414HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion17.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion914SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies36HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8275SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 112 3.24 %
Rwork0.1982 3346 -
all0.2003 3458 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.39810.0345-0.17310.7113-0.29951.08580.0731-0.0023-0.0843-0.0536-0.054-0.06830.19650.0961-0.0191-0.01790.0551-0.0046-0.1140.0115-0.09649.5441-8.4909-11.9939
22.32820.5972-0.83993.3314-1.15795.23530.01160.08590.01690.0792-0.1201-0.09420.08840.12140.1086-0.12530.0457-0.063-0.0633-0.0062-0.068924.7961-17.928317.4373
31.39010.21550.09211.26550.00490.6007-0.03310.00860.1979-0.06070.02380.21-0.017-0.11670.0093-0.0830.01380.0022-0.09790.0025-0.0621-21.52388.8372-15.1667
40-0.4144-1.31030.89131.19292.6690.00430.05790.0180.104-0.00590.0005-0.0035-0.05060.00160.01460.152-0.14420.0552-0.1482-0.0964-39.930418.625610.9395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|-4 - A|359}
2X-RAY DIFFRACTION2{A|360 - A|462}
3X-RAY DIFFRACTION3{B|-2 - B|359}
4X-RAY DIFFRACTION4{B|360 - B|459}

+
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