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- PDB-4h0p: Crystal Structure of Acetate Kinase from Cryptococcus neoformans -

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Basic information

Entry
Database: PDB / ID: 4h0p
TitleCrystal Structure of Acetate Kinase from Cryptococcus neoformans
Componentsacetate kinase
KeywordsTRANSFERASE / ATP-dependent acetate kinase / ASKHA (acetate and sugar kinase / hsc70 / actin) superfamily / Ribonuclease H-like fold
Function / homology
Function and homology information


acetate kinase / organic acid metabolic process / acetate kinase activity / acetyl-CoA biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable acetate kinase
Similarity search - Component
Biological speciesCryptococcus neoformans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.894 Å
AuthorsThaker, T.M. / Iverson, T.M.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structures of acetate kinases from the eukaryotic pathogens Entamoeba histolytica and Cryptococcus neoformans.
Authors: Thaker, T.M. / Tanabe, M. / Fowler, M.L. / Preininger, A.M. / Ingram-Smith, C. / Smith, K.S. / Iverson, T.M.
History
DepositionSep 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Sep 13, 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

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Assembly

Deposited unit
A: acetate kinase
B: acetate kinase


Theoretical massNumber of molelcules
Total (without water)96,3492
Polymers96,3492
Non-polymers00
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-45 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.370, 107.613, 79.108
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein acetate kinase


Mass: 48174.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus) / Strain: H99 serotype A / Gene: ACKA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: J9W3A6*PLUS, acetate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 18.5% PEG2000, 100 mM sodium tartrate, 50 mM ADA, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12712 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 31, 2009
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12712 Å / Relative weight: 1
ReflectionResolution: 1.89→77.95 Å / Num. all: 67072 / Num. obs: 64297 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.058 / Net I/σ(I): 27
Reflection shellResolution: 1.89→1.97 Å / Redundancy: 3 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.309 / % possible all: 89.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G99

1g99


Resolution: 1.894→38.973 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 3188 4.98 %
Rwork0.1777 --
obs0.1798 63974 95.04 %
all-64297 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.894→38.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 0 400 7034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096770
X-RAY DIFFRACTIONf_angle_d1.2339147
X-RAY DIFFRACTIONf_dihedral_angle_d13.1932474
X-RAY DIFFRACTIONf_chiral_restr0.0851033
X-RAY DIFFRACTIONf_plane_restr0.0051173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.894-1.92190.48521060.45361972X-RAY DIFFRACTION71
1.9219-1.9520.36061490.27512634X-RAY DIFFRACTION96
1.952-1.9840.29781510.21272708X-RAY DIFFRACTION98
1.984-2.01820.27271290.19662708X-RAY DIFFRACTION98
2.0182-2.05490.26241590.18912747X-RAY DIFFRACTION98
2.0549-2.09440.23131420.1842665X-RAY DIFFRACTION98
2.0944-2.13710.23911340.17712745X-RAY DIFFRACTION98
2.1371-2.18360.2261480.18172698X-RAY DIFFRACTION98
2.1836-2.23440.24571100.22922365X-RAY DIFFRACTION84
2.2344-2.29030.31021160.23382104X-RAY DIFFRACTION76
2.2903-2.35220.21151420.18632732X-RAY DIFFRACTION99
2.3522-2.42140.2531430.17562740X-RAY DIFFRACTION98
2.4214-2.49950.20241390.18212722X-RAY DIFFRACTION99
2.4995-2.58880.24471370.17992765X-RAY DIFFRACTION98
2.5888-2.69250.24811400.1872746X-RAY DIFFRACTION99
2.6925-2.8150.23711700.18282721X-RAY DIFFRACTION99
2.815-2.96330.21381450.18572720X-RAY DIFFRACTION99
2.9633-3.14890.24051360.18442771X-RAY DIFFRACTION99
3.1489-3.39190.22741470.17472737X-RAY DIFFRACTION99
3.3919-3.7330.19471290.16362704X-RAY DIFFRACTION96
3.733-4.27260.17591400.14352659X-RAY DIFFRACTION95
4.2726-5.38080.16211410.13562710X-RAY DIFFRACTION97
5.3808-38.98140.161350.15312713X-RAY DIFFRACTION95

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