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- PDB-7l4g: Crystal Structure of Acetyl-CoA synthetase in complex with acetyl... -

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Basic information

Entry
Database: PDB / ID: 7l4g
TitleCrystal Structure of Acetyl-CoA synthetase in complex with acetyl adenylate from Cryptococcus neoformans H99
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / Acetyl-coenzyme A synthetase / Acetyl Adenylate / 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
Chem-6R9 / : / PHOSPHATE ION / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Acetyl-CoA synthetase in complex with acetyl adenylate from Cryptococcus neoformans H99
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
DepositionDec 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)234,94526
Polymers232,4273
Non-polymers2,51823
Water18,4831026
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3329
Polymers77,4761
Non-polymers8578
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,42710
Polymers77,4761
Non-polymers9529
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1857
Polymers77,4761
Non-polymers7106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.390, 185.750, 84.880
Angle α, β, γ (deg.)90.00, 93.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Acetyl-coenzyme A synthetase


Mass: 77475.750 Da / Num. of mol.: 3 / Fragment: CoimA.00629.a.FS11
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: CrneC.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J9VFT1, acetate-CoA ligase

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Non-polymers , 5 types, 1049 molecules

#2: Chemical ChemComp-6R9 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate


Mass: 389.258 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H16N5O8P
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1026 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.95 % / Mosaicity: 0.2 °
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Optimization based on RigakuReagents Wizard 1/2 e8: 0.1M Potassium phosphate monobasic and sodium phosphate dibasic, pH6.2, 0.2M NaCl, 10% w/v PEG 8,000; CrneC.00629.a.FS11.PD00460 at 10 ...Details: Optimization based on RigakuReagents Wizard 1/2 e8: 0.1M Potassium phosphate monobasic and sodium phosphate dibasic, pH6.2, 0.2M NaCl, 10% w/v PEG 8,000; CrneC.00629.a.FS11.PD00460 at 10 mg/mL + 1mM TCEP (added first) + 1mM ATP + 0.25mM MgCl2; Cryo: 20% ethylene glycol; tray 318042e1, puck fgi6-3.

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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: Sep 24, 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: 2.2→50 Å / Num. obs: 110867 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 36.44 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.25 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.19RC4-4035refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFI

5ifi


Resolution: 2.2→39.06 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1991 1.8 %
Rwork0.155 --
obs0.156 110839 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15080 0 159 1026 16265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715736
X-RAY DIFFRACTIONf_angle_d0.84421453
X-RAY DIFFRACTIONf_dihedral_angle_d13.6215627
X-RAY DIFFRACTIONf_chiral_restr0.0542317
X-RAY DIFFRACTIONf_plane_restr0.0082771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.32121460.23917693X-RAY DIFFRACTION97
2.26-2.320.26041290.2127666X-RAY DIFFRACTION97
2.32-2.380.27051410.20087680X-RAY DIFFRACTION97
2.38-2.460.26061500.18627754X-RAY DIFFRACTION98
2.46-2.550.25561340.17827714X-RAY DIFFRACTION98
2.55-2.650.24811460.17287770X-RAY DIFFRACTION98
2.65-2.770.23071380.17317736X-RAY DIFFRACTION98
2.77-2.920.2141440.17067774X-RAY DIFFRACTION98
2.92-3.10.23541420.17597775X-RAY DIFFRACTION98
3.1-3.340.19341490.16117776X-RAY DIFFRACTION99
3.34-3.680.19371370.15037846X-RAY DIFFRACTION99
3.68-4.210.1531390.13317861X-RAY DIFFRACTION99
4.21-5.30.16421450.11927882X-RAY DIFFRACTION99
5.3-39.060.15221510.14317921X-RAY DIFFRACTION99
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)
16.5097-1.1209-2.2415.28842.4193.29860.3912-1.84691.58820.8863-0.4538-0.5624-0.47781.01340.10280.8198-0.36470.00551.3029-0.25690.843751.822739.876220.7848
22.03460.4710.9131.45120.63992.87830.0261-0.02790.0394-0.2072-0.02330.4568-0.0869-0.6372-0.00440.210.024-0.05590.52270.03040.4483-33.81727.2582-16.1116
31.2449-0.62460.52041.67-0.57841.21770.11770.1963-0.0763-0.304-0.0741-0.03180.27870.1563-0.03910.21720.03110.01560.297-0.03940.2085-1.4125-7.2405-10.6307
41.9439-0.32140.74451.9097-0.28062.11750.17880.1648-0.2207-0.33640.05160.32040.3814-0.1955-0.18910.2603-0.012-0.06530.2932-0.01350.2835-18.9187-5.8156-19.5749
52.04250.52830.73012.2435-0.29211.346-0.0453-0.10990.1473-0.1565-0.00770.2017-0.0747-0.19240.04310.16540.0373-0.01160.313-0.0160.2329-17.397713.9017-19.1078
63.03240.14840.48083.16442.15516.44460.010.504-0.0939-0.63420.1551-0.0708-0.09650.3428-0.18660.4565-0.0332-0.11080.48370.04550.4204-19.18897.4321-41.7912
71.035-0.14760.23511.5228-0.27720.7398-0.1002-0.0260.06670.32140.07-0.0609-0.02990.03440.03720.26770.0447-0.01120.2258-0.02890.187315.2647-13.253921.0185
84.50811.77660.08693.3391-1.98246.5257-0.09690.2395-0.17070.07850.1968-0.02160.12880.1455-0.04810.18010.0099-0.00550.1788-0.01840.19189.2489-18.456515.6567
91.1245-0.34970.55781.906-0.6951.0564-0.0561-0.0844-0.13630.41230.12540.0978-0.0006-0.0527-0.06240.30350.0440.04850.233-0.01390.21459.7041-29.334927.1272
105.4022-0.04280.41285.75860.50983.66360.03030.58440.048-0.14630.035-0.9274-0.32110.3201-0.0430.34210.02810.0150.3155-0.03840.452423.3191-47.552623.7562
110.75090.40580.07163.53081.27571.5829-0.2151-0.34460.45680.5303-0.07940.2586-0.4088-0.18360.23310.59660.1144-0.1170.4367-0.16880.50442.927629.209226.7065
121.60620.19190.3591.8914-0.30821.7804-0.1425-0.00670.38660.2008-0.055-0.1411-0.1992-0.10470.1710.25740.0413-0.07190.2016-0.06740.3526.976323.42839.682
131.4730.0410.29890.84470.06251.6952-0.14710.2180.36540.0432-0.0377-0.1937-0.21280.23910.17660.2207-0.0111-0.06520.28290.06450.399318.048521.851-0.8704
140.69690.28650.26621.64860.37150.9535-0.2224-0.14640.71580.27480.00820.0116-0.60030.00060.17460.60080.0255-0.2010.3253-0.06630.752413.954142.022914.0638
152.3554-0.0997-0.11762.35440.83512.15790.0076-0.53110.31420.5182-0.0712-0.5415-0.19290.2734-0.01460.5791-0.0293-0.23680.3897-0.01810.505224.297722.059929.169
163.1626-0.976-3.11082.98121.99866.2365-0.155-0.2960.32740.19950.0111-0.42940.04250.21170.0450.43810.008-0.14330.4499-0.11350.67934.387633.618220.1914
173.0868-0.5458-1.36374.741-0.14823.8490.0368-0.11670.7402-0.1855-0.28660.0322-0.14450.44470.19770.442-0.0264-0.04220.5740.00260.81544.496137.50597.1045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'C' AND (RESID 630 THROUGH 677 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 10 THROUGH 63 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 64 THROUGH 278 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 279 THROUGH 426 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 427 THROUGH 526 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 527 THROUGH 677 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 10 THROUGH 278 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 279 THROUGH 317 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 318 THROUGH 555 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 556 THROUGH 677 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 25 THROUGH 84 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 85 THROUGH 132 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 133 THROUGH 317 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 318 THROUGH 463 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 464 THROUGH 526 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 527 THROUGH 579 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 580 THROUGH 629 )

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