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- PDB-5u29: Crystal structure of Cryptococcus neoformans H99 Acetyl-CoA Synth... -

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Basic information

Entry
Database: PDB / ID: 5u29
TitleCrystal structure of Cryptococcus neoformans H99 Acetyl-CoA Synthetase in complex with Ac-AMS
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / NIH / NIAID / SBRI / SYNTHETASE / ACS1 / ACETYL-COA / PRX / AC-AMS / 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 / metal ion 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 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-O-(acetylsulfamoyl)adenosine / PHOSPHATE ION / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Edwards, T.E. / Potts, K.T. / Taylor, B.M.
CitationJournal: To Be Published
Title: Crystal structure of Cryptococcus neoformans H99 Acetyl-CoA Synthetase in complex with Ac-AMS
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / SSGCID / Fox III, D. / Potts, K.T. / Taylor, B.M. / Edwards, T.E. / Lorimer, D.D. / Mutz, M.W. / Krysan, D.J.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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)234,31216
Polymers232,4273
Non-polymers1,88413
Water7,188399
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0214
Polymers77,4761
Non-polymers5453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1126
Polymers77,4761
Non-polymers6375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1786
Polymers77,4761
Non-polymers7025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.280, 83.780, 101.600
Angle α, β, γ (deg.)110.33, 105.81, 87.75
Int Tables number1
Space group name H-MP1

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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 / Variant: Grubii / Plasmid: PEMB7013 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J9VFT1, acetate-CoA ligase
#2: Chemical ChemComp-7RM / 5'-O-(acetylsulfamoyl)adenosine


Mass: 388.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H16N6O7S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
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. 0.5MM AC- ...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. 0.5MM AC-AMS WAS 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 AN OPTIMIZATION SCREEN BASED ON WIZARD 1 AND 2 SCREEN CONDITION E8 (13.18% W/V PEG8,000, 0.2M NACL, 0.1M NA/K PHOSPHATE PH6) AND CRYO-PROTECTED IN 20% ETHYLENE GLYCOL. CRYSTAL ID 284335C8, ZNI9-6, APS21-ID-G), PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
PH range: 6

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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: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 72292 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 51.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.11
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.64 / Num. unique all: 21134 / CC1/2: 0.805 / % possible all: 97.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.11.1_2575: 000)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5k8f

5k8f


Resolution: 2.5→32.099 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.67
RfactorNum. reflection% reflection
Rfree0.2087 1999 2.77 %
Rwork0.1532 --
obs0.1548 72227 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.82 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15189 0 121 399 15709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715760
X-RAY DIFFRACTIONf_angle_d0.90321539
X-RAY DIFFRACTIONf_dihedral_angle_d15.189243
X-RAY DIFFRACTIONf_chiral_restr0.0582358
X-RAY DIFFRACTIONf_plane_restr0.0072792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4999-2.56240.33221420.23244975X-RAY DIFFRACTION98
2.5624-2.63160.27191420.2185000X-RAY DIFFRACTION98
2.6316-2.7090.29021420.20544994X-RAY DIFFRACTION98
2.709-2.79640.26181430.19774995X-RAY DIFFRACTION98
2.7964-2.89630.24011420.18745034X-RAY DIFFRACTION98
2.8963-3.01220.31281410.19634968X-RAY DIFFRACTION99
3.0122-3.14920.22711440.17365047X-RAY DIFFRACTION99
3.1492-3.3150.22271430.17124990X-RAY DIFFRACTION99
3.315-3.52250.21161430.16135034X-RAY DIFFRACTION99
3.5225-3.79410.20571430.14545031X-RAY DIFFRACTION99
3.7941-4.17510.19291430.13015070X-RAY DIFFRACTION99
4.1751-4.77760.17381440.11165027X-RAY DIFFRACTION99
4.7776-6.01280.14741440.12835079X-RAY DIFFRACTION99
6.0128-32.10130.18061430.144984X-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)
11.61290.05110.41583.0625-0.071.6951-0.08090.03220.0277-0.0241-0.08060.5383-0.1346-0.43950.15360.17040.0383-0.0210.5083-0.04880.4333-33.892516.03267.0179
21.3031-0.3555-0.58991.03430.28861.23680.06680.09790.082-0.2146-0.0729-0.0017-0.1776-0.14650.00440.2258-0.0175-0.03770.2485-0.00110.2587-10.29715.7019-3.1843
32.476-2.72210.24425.38372.88795.5227-0.1324-0.4860.06510.22370.10320.18460.0268-0.02140.03160.19040.006-0.01550.30050.01710.2406-6.957216.883817.9785
41.5860.3950.11874.5296-0.43162.38010.1462-0.21080.33330.3272-0.08640.085-0.6044-0.306-0.09420.3760.1216-0.04050.4156-0.06590.4823-22.995235.207712.9439
52.8265-0.47810.79811.24710.81032.7533-0.1029-0.11090.3306-0.1215-0.12530.1395-1.4535-0.8610.17540.74310.16490.04910.4412-0.03780.5474-23.948949.33764.98
63.3446-1.1967-0.36131.9991.46642.7654-0.06730.25110.3772-0.17910.0975-0.5576-0.07950.3308-0.10120.62740.03230.0450.41120.02970.8479-11.040442.35924.0297
71.0915-0.24670.08241.3382-0.01811.3716-0.164-0.4577-0.21580.30.18250.03560.28470.012-0.02140.33920.06050.02230.48070.09020.303513.096-9.698126.079
81.3828-0.018-0.17353.35581.09481.561-0.2545-0.38490.10740.1470.3518-0.26070.02950.2644-0.04690.1970.0451-0.02940.4243-0.02490.24416.90971.580619.9032
91.0397-0.35330.48320.9513-0.21271.4904-0.1242-0.6277-0.27510.40380.2187-0.06580.32980.0739-0.09210.60250.14670.0210.68080.15530.405623.2711-20.871338.3058
104.3991-1.99430.96132.5619-1.49051.469-0.24130.24310.57950.29920.0186-0.3478-0.4643-0.0290.23020.71080.0505-0.1250.94170.03130.666239.5129-10.017238.2359
111.2833-0.2497-1.13621.65740.0941.6097-0.17510.3155-0.42-0.22790.03540.14140.7234-0.30770.12470.7408-0.18750.03970.4673-0.21450.63441.3863-36.3919-32.0973
121.1485-0.079-0.11180.95370.41031.8823-0.04330.0674-0.267-0.04510.0187-0.05480.44560.1320.01730.37220.00440.0410.21260.00850.344317.9297-21.774-16.0906
132.0063-0.6789-0.3422.71690.57333.33380.050.4157-0.1819-0.4507-0.07090.1821-0.0123-0.499-0.01130.3514-0.0444-0.02880.3261-0.05230.28163.4108-13.7107-35.1356
144.62010.02330.35093.0555-1.86234.62140.18680.5797-0.4028-0.22-0.1398-0.1941-0.14690.4261-0.0940.73610.0260.13970.5139-0.13990.471724.2852-23.9087-49.3049
153.14960.7591.13692.3648-0.68023.35230.16110.1613-0.04950.16470.193-0.2184-0.36630.683-0.35870.5783-0.05990.13520.624-0.12320.471126.6834-18.4328-45.47
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 493 )
3X-RAY DIFFRACTION3chain 'A' and (resid 494 through 526 )
4X-RAY DIFFRACTION4chain 'A' and (resid 527 through 579 )
5X-RAY DIFFRACTION5chain 'A' and (resid 580 through 617 )
6X-RAY DIFFRACTION6chain 'A' and (resid 618 through 677 )
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 245 )
8X-RAY DIFFRACTION8chain 'B' and (resid 246 through 303 )
9X-RAY DIFFRACTION9chain 'B' and (resid 304 through 629 )
10X-RAY DIFFRACTION10chain 'B' and (resid 630 through 677 )
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 58 )
12X-RAY DIFFRACTION12chain 'C' and (resid 59 through 463 )
13X-RAY DIFFRACTION13chain 'C' and (resid 464 through 555 )
14X-RAY DIFFRACTION14chain 'C' and (resid 556 through 602 )
15X-RAY DIFFRACTION15chain 'C' and (resid 603 through 677 )

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