[English] 日本語
Yorodumi
- PDB-7kqz: Crystal Structure of Acetyl-CoA synthetase in complex with adenos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kqz
TitleCrystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Coccidioides immitis RS
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / Acetyl-coenzyme A synthetase / ethyl-AMP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Coccidioides immitis RS
Authors: Fox III, D. / Abendroth, J. / DeBouver, N.D. / Esan, T.E. / Hagen, T.J. / Krysan, D.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1217
Polymers78,4361
Non-polymers6866
Water5,765320
1
A: Acetyl-coenzyme A synthetase
hetero molecules

A: Acetyl-coenzyme A synthetase
hetero molecules

A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,36421
Polymers235,3073
Non-polymers2,05718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7460 Å2
ΔGint20 kcal/mol
Surface area61320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.200, 107.200, 116.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 78435.828 Da / Num. of mol.: 1 / Fragment: CoimA.00629.a.FS11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (strain RS) (fungus)
Strain: RS / Gene: CIMG_01510 / Plasmid: CoimA.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J3KJC6, acetate-CoA ligase
#2: Chemical ChemComp-WTA / 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine


Mass: 375.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Optimization condition around Molecular Dimensions MCSG1 H3: 200mM lithium acetate, 19.1% PEG 3350: CoimA.00629.a.FS11.PD00401 at 10mg/ml + 1mM TCEP + 1mM ethylAMP: tray 317942 F7: cryo: 20% ...Details: Optimization condition around Molecular Dimensions MCSG1 H3: 200mM lithium acetate, 19.1% PEG 3350: CoimA.00629.a.FS11.PD00401 at 10mg/ml + 1mM TCEP + 1mM ethylAMP: tray 317942 F7: cryo: 20% EG + ligands: puck FBB2-2.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 1, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 41174 / % possible obs: 100 % / Redundancy: 9.423 % / Biso Wilson estimate: 42.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.071 / Χ2: 0.939 / Net I/σ(I): 21.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.219.5530.5574.2430160.9030.589100
2.21-2.279.5590.4655.1329640.9330.492100
2.27-2.339.5520.3666.5228800.9610.387100
2.33-2.49.5630.298.2327940.9730.306100
2.4-2.489.570.2469.5427100.9790.26100
2.48-2.579.570.21211.0426070.9850.224100
2.57-2.679.5580.17812.8625410.9890.189100
2.67-2.789.5320.14715.6624510.9920.156100
2.78-2.99.4750.11619.3823250.9950.122100
2.9-3.049.4220.09523.3322350.9960.1100
3.04-3.219.3860.07827.4121160.9970.082100
3.21-3.49.2840.06233.1220030.9980.065100
3.4-3.639.1530.05337.6419150.9980.057100
3.63-3.939.1420.04642.3617550.9990.049100
3.93-4.39.1160.04146.216460.9990.043100
4.3-4.819.1890.03749.0814630.9990.039100
4.81-5.559.2580.03648.9813010.9990.038100
5.55-6.89.2750.03448.7411080.9990.036100
6.8-9.629.2960.02951.7486110.031100
9.62-508.650.02752.44830.9990.02998.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5ifi

5ifi


Resolution: 2.15→36.25 Å / SU ML: 0.2333 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7112
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1896 4.61 %0
Rwork0.1666 39246 --
obs0.1684 41142 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.75 Å2
Refinement stepCycle: LAST / Resolution: 2.15→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4701 0 45 320 5066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674886
X-RAY DIFFRACTIONf_angle_d0.78966662
X-RAY DIFFRACTIONf_chiral_restr0.0553723
X-RAY DIFFRACTIONf_plane_restr0.0078861
X-RAY DIFFRACTIONf_dihedral_angle_d13.19931684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.24311540.22662764X-RAY DIFFRACTION100
2.2-2.260.2678970.21242832X-RAY DIFFRACTION100
2.26-2.330.22551450.19572787X-RAY DIFFRACTION100
2.33-2.410.24791270.17462792X-RAY DIFFRACTION100
2.41-2.490.2341540.18382796X-RAY DIFFRACTION100
2.49-2.590.2066980.17892818X-RAY DIFFRACTION100
2.59-2.710.2391200.20182810X-RAY DIFFRACTION100
2.71-2.850.25011560.17252761X-RAY DIFFRACTION100
2.85-3.030.21061370.18382821X-RAY DIFFRACTION100
3.03-3.260.20211520.16922778X-RAY DIFFRACTION99.97
3.26-3.590.20441380.1672813X-RAY DIFFRACTION100
3.59-4.110.18691440.13882797X-RAY DIFFRACTION100
4.11-5.180.17291220.1362829X-RAY DIFFRACTION100
5.18-36.250.18961520.16992848X-RAY DIFFRACTION99.87
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)
11.837106826210.2217962739810.1083377290223.29650151772-0.0182964774291.727821858420.102931660546-0.195529432667-0.6943623112580.167304370508-0.102083220394-0.2279153829680.453068935674-0.2205612627840.002186026283150.312043565096-0.0434815480553-0.009712068344840.2606460159450.03504102833210.4068999101466.9196848816327.16456468481.74700959758
21.28855722313-0.4437709834230.7225755847851.72623062497-0.1282327927648.236875656150.2928388132210.534960870343-0.940193158348-0.6250333501950.121642420864-0.6146137887780.4897447541281.14449623221-0.6122233912470.740432276217-0.03732553742260.02533366608260.649962657026-0.1820902295120.94542883178519.524501261723.3868762535-10.2557161626
34.48100460235-2.172898648050.06637498926153.01895765691-0.8850704529360.3897979702210.2824731532330.192431618763-0.632814550525-0.1625429435130.370787990863-1.04325044430.5273577410820.550042096085-0.2573757055311.206754310770.127789971680.07537303862050.799052260254-0.3570689350.89204427089325.555696655122.6124383821-25.3194302457
42.092409147430.939751087517-0.3543307986532.33732772086-0.09437951194631.12547859341-0.004377401350680.0974731147887-0.437606551659-0.0106694637460.0251352598049-0.5264188799860.0744392799350.00287038645493-0.06332006704040.2330121615680.03554664153890.003001684149920.229486172869-0.01320422027850.26110280719319.041728834649.4921723028-3.09326595072
51.631520330470.769856685345-0.3136601811592.34455939978-0.0226975623980.6460112613220.0910219452878-0.142538819527-0.7667488434750.133345524712-0.082360072691-1.062714834590.170475425860.1442491490930.00309696681370.2918806957550.0426438544875-0.08770857186460.2725873966570.0519281464560.70110156850728.086514527938.1544327142.55019412222
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 455 through 517 )455 - 517445 - 507
22chain 'A' and (resid 518 through 570 )518 - 570508 - 560
33chain 'A' and (resid 571 through 637 )571 - 637561 - 618
44chain 'A' and (resid 11 through 270 )11 - 2701 - 260
55chain 'A' and (resid 271 through 454 )271 - 454261 - 444

+
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