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- PDB-6b8v: Crystal structure of adenylyl-sulfate kinase from Cryptococcus ne... -

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Basic information

Entry
Database: PDB / ID: 6b8v
TitleCrystal structure of adenylyl-sulfate kinase from Cryptococcus neoformans
ComponentsAdenylylsulfate kinase
KeywordsTRANSFERASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Adenylyl-sulfate kinase / hydrogen sulfide biosynthesis
Function / homology
Function and homology information


adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / ATP binding
Similarity search - Function
Adenylyl-sulfate kinase / Adenylylsulphate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Adenylyl-sulfate kinase
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of adenylyl-sulfate kinase from Cryptococcus neoformans
Authors: Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionOct 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 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: Adenylylsulfate kinase
B: Adenylylsulfate kinase
C: Adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0765
Polymers69,8923
Non-polymers1842
Water2,504139
1
A: Adenylylsulfate kinase
B: Adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6873
Polymers46,5952
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-19 kcal/mol
Surface area13870 Å2
MethodPISA
2
C: Adenylylsulfate kinase
hetero molecules

C: Adenylylsulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7794
Polymers46,5952
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area3430 Å2
ΔGint-16 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.680, 87.680, 173.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11C-404-

HOH

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Components

#1: Protein Adenylylsulfate kinase


Mass: 23297.422 Da / Num. of mol.: 3 / Fragment: CrneC.00830.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Gene: C362_03154 / Variant: grubii serotype A / Plasmid: CrneC.00830.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A212GZX6, UniProt: J9VMZ3*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18.6 mg/mL PS38292 against Morpheus A11: 10% w/v PEG4000, 20% v/v glycerol, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M bicine/Trizma base, pH 8.5, cryoprotection: direct, ...Details: 18.6 mg/mL PS38292 against Morpheus A11: 10% w/v PEG4000, 20% v/v glycerol, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M bicine/Trizma base, pH 8.5, cryoprotection: direct, CrneC.00830.a.B1, tray 293001, puck ltv3-1

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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: Aug 4, 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: 2.55→43.84 Å / Num. obs: 25257 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.79 % / Biso Wilson estimate: 41.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.099 / Χ2: 1.05 / Net I/σ(I): 14.76 / Num. measured all: 222005 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.628.8440.563.9418620.9680.595100
2.62-2.698.9020.4614.5917970.9750.48999.9
2.69-2.778.8530.3855.3517670.9830.40999.8
2.77-2.858.9230.3076.6116940.9870.32599.9
2.85-2.948.8150.2826.9116580.9880.29999.9
2.94-3.058.8960.2088.7516130.9940.22100
3.05-3.168.8590.16910.4215450.9960.179100
3.16-3.298.8540.14911.7514960.9960.158100
3.29-3.448.8270.11614.4614150.9970.12399.9
3.44-3.618.8020.09716.8313720.9980.10399.9
3.61-3.88.8610.07521.0713190.9980.07999.8
3.8-4.038.7320.06822.3612220.9990.07299.8
4.03-4.318.8290.06125.0211580.9990.06599.7
4.31-4.668.7570.05526.5910870.9990.05899.7
4.66-5.18.7220.05327.310010.9990.05699.7
5.1-5.78.7370.05526.298990.9990.05899.6
5.7-6.588.6670.05526.28190.9990.05999.5
6.58-8.068.5340.04727.686840.9990.0599.3
8.06-11.48.1910.03834.975390.9990.04198.9
11.4-43.847.3480.04133.753100.9990.04494.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2499: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
MoRDaphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PEY

2pey


Resolution: 2.55→43.84 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1849 7.36 %
Rwork0.1841 --
obs0.1881 25133 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 12 139 3922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073855
X-RAY DIFFRACTIONf_angle_d0.8325234
X-RAY DIFFRACTIONf_dihedral_angle_d16.772311
X-RAY DIFFRACTIONf_chiral_restr0.051618
X-RAY DIFFRACTIONf_plane_restr0.005674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.61910.35121210.2441807X-RAY DIFFRACTION99
2.6191-2.69620.36031530.2491763X-RAY DIFFRACTION99
2.6962-2.78320.30481420.22861764X-RAY DIFFRACTION99
2.7832-2.88270.30161310.21581780X-RAY DIFFRACTION100
2.8827-2.99810.30691310.23191797X-RAY DIFFRACTION99
2.9981-3.13450.2841540.21811781X-RAY DIFFRACTION99
3.1345-3.29970.28061370.24241774X-RAY DIFFRACTION100
3.2997-3.50630.26941510.21341780X-RAY DIFFRACTION100
3.5063-3.77690.25281670.18211751X-RAY DIFFRACTION100
3.7769-4.15670.21281150.16411831X-RAY DIFFRACTION100
4.1567-4.75760.18971650.13491780X-RAY DIFFRACTION100
4.7576-5.99160.19331430.14821807X-RAY DIFFRACTION100
5.9916-43.84650.1771390.15891869X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -0.7226 Å / Origin y: 18.8312 Å / Origin z: -25.3298 Å
111213212223313233
T0.3595 Å2-0.0507 Å2-0.0003 Å2-0.2499 Å2-0.0379 Å2--0.4424 Å2
L1.5869 °2-0.0328 °2-0.1427 °2-0.189 °2-0.0738 °2--0.4925 °2
S0.0359 Å °-0.1162 Å °0.1048 Å °0.039 Å °0.0152 Å °-0.0377 Å °-0.1362 Å °0.0608 Å °-0.0599 Å °
Refinement TLS groupSelection details: all

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