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- PDB-5vpv: Crystal structure of Apo Cryptococcus neoformans H99 Acetyl-CoA S... -

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Basic information

Entry
Database: PDB / ID: 5vpv
TitleCrystal structure of Apo Cryptococcus neoformans H99 Acetyl-CoA Synthetase with an Acetylated Active Site Lysine
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / SSGCID / NIH / NIAID / SBRI / UW / Beryllium / 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
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
PHOSPHATE ION / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Davies, D.R. / Calhoun, B.
CitationJournal: to be published
Title: Crystal structure of Apo Cryptococcus neoformans H99 Acetyl-CoA Synthetase with an Acetylated Active Site Lysine
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Fox III, D. / Davies, D.R. / Calhoun, B. / Edwards, T.E. / Lorimer, D.D. / Mutz, M.W. / Krysan, D.J.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release

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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)233,57214
Polymers232,5503
Non-polymers1,02211
Water12,304683
1
A: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9806
Polymers77,5171
Non-polymers4635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7964
Polymers77,5171
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7964
Polymers77,5171
Non-polymers2793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.980, 176.980, 159.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-882-

HOH

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Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 77516.781 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: RigakuReagents Morpheus H3: 10.0% w/v PEG4,000, 20% glycerol, 0.02M amino acid mix, 0.1M MES/imidazole pH6.5; CrneC.00629.a.FS11.PD00402 at 10.0mg/ml; Crystals were directly cryo-protected. Puck lrm5-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2017 / 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: 2.6→49.277 Å / Num. obs: 78331 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.18
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 5.02 / CC1/2: 0.952 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_2744refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.277 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.97
RfactorNum. reflection% reflection
Rfree0.2162 3904 4.99 %
Rwork0.1561 --
obs0.1591 78263 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.12 Å2 / Biso mean: 36.0449 Å2 / Biso min: 3.68 Å2
Refinement stepCycle: final / Resolution: 2.6→49.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14119 0 63 685 14867
Biso mean--73.66 34.5 -
Num. residues----1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714623
X-RAY DIFFRACTIONf_angle_d0.84319927
X-RAY DIFFRACTIONf_chiral_restr0.0532135
X-RAY DIFFRACTIONf_plane_restr0.0062575
X-RAY DIFFRACTIONf_dihedral_angle_d15.8448610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.63170.30691340.193626212755100
2.6317-2.6650.29471310.184826252756100
2.665-2.70010.24061260.168326152741100
2.7001-2.73710.28231390.170426272766100
2.7371-2.77620.24641400.166626532793100
2.7762-2.81760.2371430.166625782721100
2.8176-2.86160.22171530.161226232776100
2.8616-2.90860.23781340.168726422776100
2.9086-2.95870.25451410.176626002741100
2.9587-3.01250.27171320.183326382770100
3.0125-3.07040.24421580.17926092767100
3.0704-3.13310.27811260.178226382764100
3.1331-3.20120.23531380.17526352773100
3.2012-3.27570.24031350.162626492784100
3.2757-3.35760.25271220.16726522774100
3.3576-3.44830.22551520.168426212773100
3.4483-3.54980.2151600.163426182778100
3.5498-3.66430.2271520.158826432795100
3.6643-3.79520.18151170.149426802797100
3.7952-3.94710.20141370.138226412778100
3.9471-4.12670.20611500.135626712821100
4.1267-4.34410.1691360.1226592795100
4.3441-4.61610.16151420.117326642806100
4.6161-4.97220.17211340.116227052839100
4.9722-5.4720.15761210.12627132834100
5.472-6.26240.20851240.155727392863100
6.2624-7.88480.22541670.17427302897100
7.8848-49.28610.20431600.18742870303099
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)
10.6184-0.1445-0.10121.18170.37690.89620.02140.02840.0008-0.15080.0949-0.132-0.00270.1132-0.10650.1843-0.00520.02850.1628-0.0140.209762.6829-21.2066-46.3439
20.4911-0.17920.03460.6615-0.35290.9938-0.0368-0.03070.06340.10690.07290.0571-0.2629-0.0804-0.03450.2682-0.0050.00640.15520.00920.229529.588226.5771-43.9975
30.8485-0.1372-0.1270.81810.11360.7238-0.0899-0.1947-0.0490.17040.09050.07640.0570.0242-0.00080.24050.06870.00770.2704-0.01140.188534.2046-0.4337-1.9775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 13 through 681)A13 - 681
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 679)B2 - 679
3X-RAY DIFFRACTION3(chain 'C' and resid 25 through 543)C25 - 543

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