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- PDB-5k85: Crystal Structure of Acetyl-CoA Synthetase in Complex with Adenos... -

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Basic information

Entry
Database: PDB / ID: 5k85
TitleCrystal Structure of Acetyl-CoA Synthetase in Complex with Adenosine-5'-propylphosphate and Coenzyme A from Cryptococcus neoformans H99
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / NIH / NIAID / SYNTHETASE / ACS1 / ACETYL-COA / PRX / PROPYL-AMP / COENZYME A / COA / 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, C-terminal domain / ANL, N-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, C-terminal domain / ANL, N-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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / 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: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Delker, S.L. / Potts, K.T. / Lorimer, D.D. / Edwards, T.E. / Mutz, M.W. / SSGCID
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF ACETYL-COA SYNTHETASE IN COMPLEX WITH ADENOSINE-5'-PROPYLPHOSPHATE AND COENZYME A FROM CRYPTOCOCCUS NEOFORMANS H99
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / SSGCID / Fox III, D. / Delker, S.L. / Potts, K.T. / Numa, M.M. / Edwards, T.E. / Lorimer, D.D. / Mutz, M.W. / Krysan, D.J.
History
DepositionMay 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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

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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)235,07818
Polymers232,4273
Non-polymers2,65115
Water13,349741
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3009
Polymers77,4761
Non-polymers8248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0845
Polymers77,4761
Non-polymers6084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6954
Polymers77,4761
Non-polymers1,2193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 186.090, 85.320
Angle α, β, γ (deg.)90.00, 93.80, 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
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

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Non-polymers , 5 types, 756 molecules

#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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.42 %
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 2MM 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 271854A7 MNJ8-1 APS21-ID-G), PH 6.20, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 97753 / % possible obs: 97.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 43.56 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.14
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.01 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(DEV_2443: ???)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFI

5ifi


Resolution: 2.3→27.57 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / Phase error: 22.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1994 2.04 %
Rwork0.179 --
obs0.179 97663 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.65 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14444 0 171 741 15356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615225
X-RAY DIFFRACTIONf_angle_d0.75320807
X-RAY DIFFRACTIONf_dihedral_angle_d14.9828899
X-RAY DIFFRACTIONf_chiral_restr0.052241
X-RAY DIFFRACTIONf_plane_restr0.0062685
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)
11.3355-0.63120.46681.6961-0.65711.28220.14390.1229-0.1124-0.34030.01480.19390.2887-0.0434-0.13770.245-0.0164-0.01660.26930.00090.2364-9.4118-4.7522-13.1884
21.77120.75640.44192.7154-0.47721.33280.08020.0872-0.0507-0.38220.12220.40330.1711-0.2095-0.16580.23120.0024-0.05670.3540.04670.3193-20.93739.0289-23.9011
34.89951.44550.67755.30962.10023.0740.03770.3637-0.2621-0.86360.2136-0.06380.1664-0.0178-0.24010.6531-0.0546-0.10920.54490.05670.3754-19.05934.8695-45.7069
40.8371-0.18940.22512.015-0.51990.7715-0.105-0.0909-0.03580.42270.0789-0.0491-0.04370.02380.02470.30970.06660.0150.2604-0.01420.19113.3726-19.256723.3157
53.118-0.53620.88764.46480.63643.19060.02650.1987-0.0066-0.23890.2792-0.6924-0.40170.3259-0.2870.3717-0.04570.0680.3026-0.0650.371518.1501-47.705924.3451
61.71860.58790.01641.4930.85010.6164-0.082-0.35520.84590.3276-0.29650.3715-0.5711-0.12630.35951.16950.1968-0.28720.711-0.3010.87514.799836.823629.6334
71.3753-0.19420.26481.1829-0.17621.1047-0.22120.17120.46130.1651-0.0719-0.3355-0.27590.15570.23950.2587-0.0238-0.110.29520.07010.476914.304921.59891.0015
80.34830.5601-0.20030.9466-0.23980.5955-0.2774-0.08820.72940.6132-0.0665-0.2686-0.74930.15330.25710.7848-0.0496-0.3790.3853-0.01170.910115.087337.540212.4224
91.64780.07510.12992.83740.9961.3421-0.1618-0.44520.59520.3565-0.0709-0.3221-0.58980.11870.12350.7824-0.0203-0.32760.4911-0.08640.683323.346427.458228.382
101.07831.85741.05193.92970.02675.5714-0.0918-0.19530.6609-0.0196-0.013-0.221-0.11240.53380.09460.51520.02920.01280.78950.0260.997644.400333.76678.5484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 382 )
2X-RAY DIFFRACTION2chain 'A' and (resid 383 through 555 )
3X-RAY DIFFRACTION3chain 'A' and (resid 556 through 681 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 526 )
5X-RAY DIFFRACTION5chain 'B' and (resid 527 through 681 )
6X-RAY DIFFRACTION6chain 'C' and (resid 25 through 63 )
7X-RAY DIFFRACTION7chain 'C' and (resid 64 through 278 )
8X-RAY DIFFRACTION8chain 'C' and (resid 279 through 443 )
9X-RAY DIFFRACTION9chain 'C' and (resid 444 through 551 )
10X-RAY DIFFRACTION10chain 'C' and (resid 552 through 630 )

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