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- PDB-7knp: Crystal structure of Acetyl-CoA synthetase in complex with adenos... -

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Basic information

Entry
Database: PDB / ID: 7knp
TitleCrystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-butylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / 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 / mitochondrion / 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 / 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
PHOSPHATE ION / 5'-O-[(S)-butoxy(hydroxy)phosphoryl]adenosine / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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'-butylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)
Authors: Abendroth, J. / Fox III, D. / Esan, T.E. / Hagen, T.J. / Krysan, D.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.journal_abbrev
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)234,57220
Polymers232,4273
Non-polymers2,14517
Water14,754819
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint22 kcal/mol
Surface area60920 Å2
Unit cell
Length a, b, c (Å)72.250, 184.660, 85.130
Angle α, β, γ (deg.)90.000, 93.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: Crnec.00629.a.FS11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase
#2: Chemical ChemComp-WT7 / 5'-O-[(S)-butoxy(hydroxy)phosphoryl]adenosine


Mass: 403.328 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H22N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: Optimization screen around RigakuReagents Wizard screen 1/2, condition e8: 100mM potassium / sodium phosphate dibasic pH 5.8, 200mM NaCl, 12.73% (w/V) PEG 8000: CrneC.00629.a.FS11.PD00460 at ...Details: Optimization screen around RigakuReagents Wizard screen 1/2, condition e8: 100mM potassium / sodium phosphate dibasic pH 5.8, 200mM NaCl, 12.73% (w/V) PEG 8000: CrneC.00629.a.FS11.PD00460 at 10mg/ml + 1mM TCEP + 1mM butyl-AMP: tray 317934 a7: cryo: 20% EG + compounds: puck: ffb2-5

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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: 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: 2.25→50 Å / Num. obs: 103490 / % possible obs: 98.4 % / Redundancy: 3.863 % / Biso Wilson estimate: 42.752 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.105 / Χ2: 0.907 / Net I/σ(I): 10.14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.9090.5472.675970.810.63497.9
2.31-2.373.9060.4593.0674040.8590.53297.9
2.37-2.443.9050.3773.6872010.8980.43798.1
2.44-2.523.9030.3124.3870210.9280.36198.1
2.52-2.63.9010.2764.8868180.940.3298.3
2.6-2.693.8970.2325.7465930.9560.2798.3
2.69-2.793.8940.1896.7663860.9710.21998.4
2.79-2.93.8830.1558.161080.9770.1898.5
2.9-3.033.8710.139.3559090.9830.15198.5
3.03-3.183.8610.10111.6155940.9880.11898.7
3.18-3.353.8470.08313.6853540.990.09698.6
3.35-3.563.8280.07215.3250960.9910.08498.7
3.56-3.83.830.06616.8847650.9930.07698.7
3.8-4.113.8170.06118.4144310.9930.07198.6
4.11-4.53.8050.05719.6741070.9930.06698.7
4.5-5.033.8010.05620.3236760.9930.06598.9
5.03-5.813.7960.05720.1432870.9930.06699.2
5.81-7.123.7870.05720.1528100.9930.06699.4
7.12-10.063.7590.0572221450.9930.06699.1
10.06-503.6090.05722.3311880.9930.06797.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5ifi
Resolution: 2.25→40.26 Å / SU ML: 0.2725 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2160 2.09 %0
Rwork0.1756 101290 --
obs0.1764 103450 98.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.29 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13942 0 139 819 14900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006914519
X-RAY DIFFRACTIONf_angle_d0.823119819
X-RAY DIFFRACTIONf_chiral_restr0.05312141
X-RAY DIFFRACTIONf_plane_restr0.00882562
X-RAY DIFFRACTIONf_dihedral_angle_d13.86375123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.25681480.2356700X-RAY DIFFRACTION98
2.3-2.360.28891380.22996679X-RAY DIFFRACTION97.95
2.36-2.420.26021630.22236677X-RAY DIFFRACTION97.94
2.42-2.50.24561300.21216764X-RAY DIFFRACTION98.12
2.5-2.580.2771460.20816738X-RAY DIFFRACTION98.26
2.58-2.670.25551410.20026704X-RAY DIFFRACTION98.32
2.67-2.770.25971480.20116729X-RAY DIFFRACTION98.31
2.77-2.90.24511420.19966763X-RAY DIFFRACTION98.54
2.9-3.050.23261640.20086724X-RAY DIFFRACTION98.61
3.05-3.240.27351430.18826753X-RAY DIFFRACTION98.63
3.24-3.50.20371130.17636811X-RAY DIFFRACTION98.76
3.5-3.850.21521360.16946805X-RAY DIFFRACTION98.61
3.85-4.40.17371630.14056734X-RAY DIFFRACTION98.61
4.4-5.540.16871310.13866844X-RAY DIFFRACTION98.98
5.54-40.260.16331540.166865X-RAY DIFFRACTION98.91
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.405791043740.09798643713580.09550901535011.36240159701-0.3673499321380.847139411310.2429977740270.0810749670234-0.238352694384-0.5188032314640.231336531341.07884881650.20261003637-0.422933872724-0.05285646393970.279418946399-0.0312048835185-0.2102357975610.5213966857580.2145794306771.05391090028-33.72689374516.89541131491-16.9453513197
21.47763627243-0.7440658603480.486764534792.35036350811-1.073555024041.038707315740.135300302604-0.00467919708344-0.242071512383-0.1408538658320.06095805208380.425460422880.177461528943-0.0200344752332-0.1507974015640.1771011632660.0002428384958150.002083582117570.293996410091-0.002759796894840.246147698223-7.09299327356-4.42467096418-5.67220493573
30.611555438533-0.7177965587450.1277834389351.41837259347-0.5392341042690.3245459749610.3708890945940.404956351173-0.019477038619-0.834705305603-0.374911872064-0.01538036328130.4247576206710.3072746226920.003319294773410.5824922526250.1987514561110.06066912862330.554384728961-0.03155998019940.2181088089244.7149136102-8.10150477192-18.1363847317
40.898049866686-0.2059024800250.4320547546190.921950760111-0.4280401751490.3587103332510.4428613893210.205509678574-0.62532684082-0.8261196201930.1390741974691.142937526240.55334016312-0.127661155832-0.09123148297950.509893985717-0.0393505624796-0.4072790632620.423408652199-0.006884653803430.767424361189-22.1947299594-5.53122479092-21.0096375649
51.16294322034-0.6530431486080.762924864062.49769331375-1.013138772851.692467924550.07037610824250.04058381741620.0414284572683-0.267003149672-0.01717956557790.259401863054-0.01503843582540.0600864530678-0.1601503000840.1994812018570.002196714904040.01626396153780.3245291165060.01132865533530.287266278084-13.49302113618.8837564489-19.7933638013
63.354704050470.1935146539780.9191230213822.54409932921.78923190913.468688466120.0555626828490.62959028113-0.115816547284-1.198341167430.1760536431360.693821059085-0.0892495911388-0.0444694867179-0.1193398295920.737821863728-0.0473613356853-0.2996781827980.4801448403140.06649539749790.605745997942-22.542850175411.8737124008-36.2491950023
72.2949891020.4612453437191.035306403310.4339412918831.050305608043.20707611314-0.01882169167980.446959425739-0.280640131172-1.006087320940.1582453908420.565393372928-0.1132968227620.0931985080143-0.1399810599811.48869964519-0.0551987753302-0.6099589359380.669897916764-0.01677231100360.93391912946-23.49684867814.1344333731-50.2011224479
87.976440000050.2954736266171.450343604372.947670281430.8007772917231.310887871010.07664610698440.253520125637-0.268164635339-0.7444086542760.1025542403710.08156974849610.230046634236-0.149240685048-0.1303521225731.044297906020.00494608016179-0.3027145571640.7589296766310.001835984334110.5473604753-12.2409185515.096266067-44.7326253221
90.530088522613-0.60769555043-0.08372358093930.7478879501260.1521060367640.752858086743-0.091732796938-0.330491696867-0.2217221912380.9402604807350.4748572816790.566873231062-0.0352927905308-0.2533563227680.4209309251741.043081735620.3754908134660.5150433846250.6681097646290.2942642816070.499965904219-1.03652815361-30.089878958936.6141854777
101.56424160552-0.527660241070.7193159365562.49909784591-0.6816551348121.21552796606-0.194436415365-0.02918004396930.2180817469130.6637075443190.0376729905421-0.46658796015-0.1947909764040.1972006995990.1079133883040.4325224974710.0413167812276-0.08972973544360.339949907911-0.00926584463430.26000595021719.5943553462-9.1956764962316.2527493822
110.269892891866-0.03880897611490.1370725002811.27078868029-0.4109907748710.329451106567-0.333527289193-0.112456186823-0.02554107669091.313662510170.251902211122-0.278928707798-0.382105867203-0.0765442408202-0.03526037807440.9442373996610.189719731735-0.06221529230960.434463156958-0.004110217472840.18662461757416.2461488628-22.501910924430.9050694961
120.660809912926-0.8538188339910.3322266531131.42889009369-0.5205829356373.91747401001-0.00095255426572-0.195063006257-0.3675748620070.383695407990.3300060265060.755445342270.0984243591624-0.267499831274-0.2405435903230.3880848774760.05952770996580.1538347720660.3268000240180.09011328009340.3968924526971.67303837234-30.565190309917.5806739838
132.44755199328-0.41671052009-0.3068322123524.8634738423-0.3298976381842.394517399710.07916414897390.0563302659926-0.04045799004830.4486423038730.168051533625-0.0908647801069-0.3112772170090.0172457010239-0.1772930571190.3493667703890.01527592182760.01717268040390.2586709373080.01895654937140.23231014562215.3817492333-48.734755944826.3735761056
141.92432269173.38940529145-1.606543033777.02946231849-3.896013177522.68826094161-0.00425764375410.3610983597990.00706960417764-0.237613535896-0.219625819751-1.06714505084-0.5293180216810.4256753879990.2066586727180.505837647869-0.04282014522420.08637023200830.478231995087-0.007723524610210.60112279523527.6032667524-44.930374306419.2969396004
150.339872253369-0.001084646816230.2146170325970.775807671790.481949525010.6466508091-0.256180515228-0.05677794316020.54734936766-0.116105163559-0.08910787746750.159113764765-0.656625220753-0.2490240481410.5488872500811.7805328660.438174443131-0.6325913199410.783214728587-0.418093464611.009153385393.5496227786939.509149311927.2495361119
161.67607531827-0.7334720631940.1382161220491.97948072418-0.09837184536440.499057706703-0.3164077043370.2194107751410.66302090650.699207156612-0.148096966792-0.908473788175-0.3621669267660.07848746041390.1769986884270.30650503775-0.0617747659368-0.1986029125640.3642595332540.1305819693010.66322754451713.980611219421.42839607750.977127618467
171.132607904691.40102423240.3848295871171.90350162307-0.06306269102661.96822660559-0.248347176158-0.123654399630.4897730209060.627505439524-0.175743394175-0.532540365027-0.5165720556470.329096586860.2005064092560.638045675474-0.00268362221112-0.3217915102120.378191297887-0.01114889243490.619886481915.869155683321.099124009113.8861619564
180.5833972485150.3236074171130.305302240760.3073156540690.01962785724720.409925482206-0.326766037163-0.006157867126941.162769942340.689802784763-0.14957661265-0.627937841988-0.925396311394-0.0001528124616490.2206148146580.878879326197-0.0352128874093-0.4433999770730.3724367943790.03008098922281.097820468811.957262150338.68529105326.90133498551
193.58098548954-0.3294153838330.9302645846470.2040419748310.2067083096650.713664122069-0.107645360072-0.02864378241520.5560088846770.388641352063-0.0130859665458-0.509771920455-0.5546080136840.2492137560890.09007571196291.58453885651-0.105321046996-0.814532517660.433027118472-0.07893315866961.6155687798917.674688511149.448074076414.1375359436
200.7216272654480.0973535119104-0.6521668698930.015664556936-0.0849584668920.5987907452810.0506632767692-0.39911997840.3480876140630.1315143197190.07310190461890.0732657187919-0.5695410248620.04099608558980.4042230494111.516479345570.0352543942097-0.9272108933580.53588663328-0.2923243441931.2884695542715.062846998738.211181137822.3532097789
210.296907595178-0.262220577603-0.1365008026550.5222434568030.1443957685050.454263187208-0.211046016122-0.5159787973010.4437361160670.6959777082040.0341460047613-0.48422169708-0.3969708635590.0872115889983-0.1184900576381.38886268617-0.013396396048-0.7877069050260.557140172105-0.3400952245151.0272152256921.999628700524.491524382128.7319020644
220.2267056004410.1118195380030.07704574449260.167799814357-0.1876390212440.4626346002320.122899407161-0.6339636720030.2576025997630.4888778162640.0188224578479-0.178048560745-0.292278372478-0.1240208853090.8596462631411.256556979-0.0575739838251-1.058274357460.692308339764-0.2602029327111.1819421606726.543247805325.064695526627.8539881595
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 63 )AA10 - 631 - 54
22chain 'A' and (resid 64 through 182 )AA64 - 18255 - 173
33chain 'A' and (resid 183 through 303 )AA183 - 303174 - 292
44chain 'A' and (resid 304 through 463 )AA304 - 463293 - 452
55chain 'A' and (resid 464 through 526 )AA464 - 526453 - 515
66chain 'A' and (resid 527 through 579 )AA527 - 579516 - 568
77chain 'A' and (resid 580 through 617 )AA580 - 617569 - 606
88chain 'A' and (resid 618 through 676 )AA618 - 676607 - 653
99chain 'B' and (resid 10 through 63 )BH10 - 631 - 54
1010chain 'B' and (resid 64 through 278 )BH64 - 27855 - 269
1111chain 'B' and (resid 279 through 432 )BH279 - 432270 - 419
1212chain 'B' and (resid 433 through 526 )BH433 - 526420 - 513
1313chain 'B' and (resid 527 through 617 )BH527 - 617514 - 601
1414chain 'B' and (resid 618 through 678 )BH618 - 678602 - 658
1515chain 'C' and (resid 26 through 58 )CP26 - 581 - 33
1616chain 'C' and (resid 59 through 278 )CP59 - 27834 - 253
1717chain 'C' and (resid 279 through 317 )CP279 - 317254 - 288
1818chain 'C' and (resid 318 through 382 )CP318 - 382289 - 353
1919chain 'C' and (resid 383 through 426 )CP383 - 426354 - 397
2020chain 'C' and (resid 427 through 461 )CP427 - 461398 - 432
2121chain 'C' and (resid 462 through 507 )CP462 - 507433 - 478
2222chain 'C' and (resid 508 through 540 )CP508 - 540479 - 511

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