[English] 日本語
Yorodumi
- PDB-5ifi: CRYSTAL STRUCTURE OF ACETYL-COA SYNTHETASE IN COMPLEX WITH ADENOS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ifi
TitleCRYSTAL STRUCTURE OF ACETYL-COA SYNTHETASE IN COMPLEX WITH ADENOSINE-5'-PROPYLPHOSPHATE FROM CRYPTOCOCCUS NEOFORMANS H99
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / NIH / NIAID / SBRI / UW / BERYLLIUM / SYNTHETASE / ACS1 / PRX / PROPYL-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 / metal ion binding / cytosol
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / ANL, C-terminal domain / 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. ...Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / ANL, C-terminal domain / 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 / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / SSGCID / Fox III, D. / Edwards, T.E. / Lorimer, D.D. / Mutz, M.W.
CitationJournal: To Be Published
Title: Crystal structure of Acetyl-CoA Synthetase in complex with Adenosine-5'-propylphosphate from Cryptococcus neoformans H99
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / SSGCID / Fox III, D. / Edwards, T.E. / Potts, K.T. / Lorimer, D.D. / Mutz, M.W. / Numa, M.M.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,09228
Polymers232,4273
Non-polymers2,66525
Water17,457969
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,48612
Polymers77,4761
Non-polymers1,01011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,61712
Polymers77,4761
Non-polymers1,14211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9894
Polymers77,4761
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.460, 185.550, 84.890
Angle α, β, γ (deg.)90.00, 93.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 77475.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_00797 / Plasmid: PEMB7013 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase
#2: Chemical ChemComp-PRX / ADENOSINE-5'-MONOPHOSPHATE-PROPYL ESTER / ADENOSINE-5'-PROPYLPHOSPHATE


Mass: 389.301 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H20N5O7P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: ACETYL COA SYNTHETASE FROM CRYPTOCOCCUS NEOFORMANS (CRNEC.00629.A.FS11.PD00402) AT 10MG/ ML (IN 10 MM TRIS, PH = 7.5, 20 MM NACL) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. 1MM ...Details: ACETYL COA SYNTHETASE FROM CRYPTOCOCCUS NEOFORMANS (CRNEC.00629.A.FS11.PD00402) AT 10MG/ ML (IN 10 MM TRIS, PH = 7.5, 20 MM NACL) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. 1MM ADENOSINE-5'- PROPYLPHOSPHATE AND COA WERE ADDED TO THE PROTEIN SOLUTION AND INCUBATED FOR 5 MINUTES BEFORE SETTING UP TRIALS. CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND IN WIZARD 1 AND 2 SCREEN CONDITION E8 (10% W/V PEG8,000, 0.1M NA/K PHOSPHATE PH6.2) AND CRYO-PROTECTED IN 20% ETHYLENE GLYCOL. CRYSTAL ID 269918E8 DIT9-1 APS 21-ID-F), PH 6.20, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 159980 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 34.78 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.96
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.47 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(DEV_2328: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RY2

1ry2


Resolution: 1.95→41.84 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / Phase error: 24.45
RfactorNum. reflection% reflection
Rfree0.213 8023 5.02 %
Rwork0.185 --
obs0.186 159842 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.33 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14105 0 170 969 15244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614805
X-RAY DIFFRACTIONf_angle_d0.79120220
X-RAY DIFFRACTIONf_dihedral_angle_d14.5068642
X-RAY DIFFRACTIONf_chiral_restr0.1442194
X-RAY DIFFRACTIONf_plane_restr0.0062614
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)
11.25110.03420.21130.92620.13811.14760.13040.015-0.1069-0.33630.26250.57320.1061-0.6293-0.07610.1225-0.0933-0.09950.60310.25330.5981-33.60836.9727-16.1587
21.1019-0.72320.47282.3643-0.57161.00840.10960.1476-0.0499-0.3613-0.0290.07350.24890.1077-0.10180.18590.01810.00950.262-0.0130.1575-2.6446-5.4534-11.1736
31.2534-0.50190.55571.6402-0.69251.18270.19280.1851-0.2024-0.49610.06640.38230.4472-0.0838-0.16010.3152-0.0276-0.09340.2868-0.00410.239-13.5203-7.8192-18.2454
40.81510.22570.41092.1855-0.6751.29280.03350.00620.0201-0.17980.07910.27390.0189-0.1456-0.08950.13020.01270.010.3020.04570.2607-17.495113.8927-19.349
51.50960.21120.70152.13621.0022.30280.07410.3989-0.1062-0.78780.15750.22040.16210.1806-0.21120.6133-0.0117-0.16510.51780.06390.3815-20.04797.9049-41.9767
60.8674-0.54950.06251.21340.77180.8214-0.1118-0.3068-0.30861.00620.49390.2677-0.1278-0.28850.5180.71910.13880.33510.39720.15470.3029-0.2872-30.499238.1783
70.4828-0.5841-0.02061.8885-0.61090.9203-0.1399-0.07280.08530.5440.15450.1064-0.1461-0.06910.00120.33660.0790.06760.2519-0.00610.16334.4607-9.778921.3873
82.18-0.49650.2991.9084-0.25721.1151-0.13690.1190.2240.2672-0.0229-0.4912-0.03250.25560.13910.22110.0136-0.06940.28110.03420.292526.754-9.293214.379
91.91280.47120.03841.4808-1.02652.39-0.1177-0.0419-0.0830.39150.16140.0673-0.03750.02380.05270.22460.07090.07050.19710.00640.13858.3654-17.125416.5396
100.15180.0170.37751.4611-0.47661.2298-0.247-0.1240.08571.05180.1063-0.2763-0.27290.04980.1180.59510.0942-0.09710.28120.00010.205418.42-18.724932.2962
111.347-0.04520.31961.4411-0.05351.3505-0.174-0.3137-0.17331.09210.1756-0.2102-0.20290.04220.01510.6960.0842-0.0510.2990.0550.263917.9698-31.873238.899
120.8613-0.49290.63282.3176-1.41362.27050.0162-0.1181-0.20940.00520.16730.44950.2506-0.2528-0.20910.28040.00960.07810.22540.02450.26491.7467-30.673117.6869
132.6906-0.58440.87845.14290.26491.85660.04860.0775-0.2218-0.08030.23110.1038-0.1562-0.0122-0.19840.3596-0.00550.06810.23980.02570.243810.3048-45.185124.2368
143.68330.12260.9455.78570.27573.0074-0.01110.1122-0.2850.28780.1941-0.69950.02670.1095-0.34030.29590.00580.0010.2262-0.04490.393321.3881-54.181328.4186
151.99640.76640.26131.5541-1.00651.4657-0.04480.53840.0273-0.64110.2994-0.8719-1.02140.5704-0.25380.8047-0.21360.30920.5671-0.17720.668624.4402-45.974420.24
160.71890.2737-0.4020.51630.17030.5335-0.3151-0.61370.38340.93330.1379-0.2064-0.5855-0.22930.11270.85680.1585-0.20680.4478-0.16610.38925.94820.238325.0709
170.5589-0.13710.04050.85240.00841.3283-0.33270.22790.48190.23770.0132-0.3582-0.6816-0.11450.21980.37880.045-0.15870.24290.03170.49213.945130.92930.9624
181.2112-0.35380.03570.2272-0.07681.1852-0.22250.33560.53970.2291-0.1779-0.5336-0.34130.25860.23350.1849-0.0804-0.09910.34880.19340.581718.477821.8391-5.2477
190.32840.21160.5181.5153-0.56451.4716-0.3686-0.12390.66550.6888-0.0533-0.4271-0.66720.07130.26070.56740-0.27650.2749-0.04190.589913.386326.856712.6466
200.10310.18410.10610.8738-0.28880.626-0.2984-0.03880.78560.6243-0.1209-0.2513-1.08740.22230.00731.1346-0.0408-0.65090.08330.06181.209614.086646.33177.4546
210.4707-0.0719-0.26781.25850.32951.5845-0.1266-0.19250.72490.3267-0.0982-0.2853-1.06050.06230.21681.2167-0.0098-0.55920.3747-0.19521.020516.961739.989520.9378
221.16910.3053-0.81141.49510.3830.808-0.3051-0.56450.56060.4383-0.0585-0.3149-0.64740.06140.14841.25690.0789-0.51750.569-0.23420.853921.07231.060633.9102
231.13910.80020.22851.3678-0.11810.128-0.1764-0.43270.48060.5641-0.15-0.4077-0.6320.17920.04960.7974-0.0193-0.41090.4241-0.05960.669124.92422.562825.9375
248.30730.1353-5.16492.45642.58666.11630.2121-0.02971.2212-0.38810.182-0.1496-0.57290.1059-0.27990.80090.1411-0.07020.8480.00611.164341.897431.587812.4425
255.55041.48081.1313.9626-0.21793.7704-0.124-0.00031.5615-0.38750.16980.091-0.02490.6238-0.13030.63830.07370.01230.90340.10321.22444.725135.47736.0089

+
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