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- PDB-3cr7: Crystal structure of N-terminal truncation of APS Kinase from Pen... -

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Basic information

Entry
Database: PDB / ID: 3cr7
TitleCrystal structure of N-terminal truncation of APS Kinase from Penicillium chrysogenum: Ternary structure with ADP and PAPS
ComponentsAdenylyl-sulfate kinase
KeywordsTRANSFERASE / APS kinase / Adenylylsulfate kinase / sulfate metabolism / Nucleotide 2 kinase / Amino-acid biosynthesis / ATP-binding / Cysteine biosynthesis / Methionine biosynthesis / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / methionine biosynthetic process / ATP binding / cytosol
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
ADENOSINE-5'-DIPHOSPHATE / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / Adenylyl-sulfate kinase
Similarity search - Component
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGay, S.C. / Segel, I.H. / Fisher, A.J.
CitationJournal: To be Published
Title: Truncated APS kinase from Pencillium chrysogenum: Insight into the function of the N-terminal helix
Authors: Gay, S.C. / Segel, I.H. / Fisher, A.J.
History
DepositionApr 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylyl-sulfate kinase
B: Adenylyl-sulfate kinase
C: Adenylyl-sulfate kinase
D: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,24613
Polymers89,4164
Non-polymers2,8309
Water8,917495
1
A: Adenylyl-sulfate kinase
B: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1417
Polymers44,7082
Non-polymers1,4335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-39.3 kcal/mol
Surface area16180 Å2
MethodPISA
2
C: Adenylyl-sulfate kinase
D: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1056
Polymers44,7082
Non-polymers1,3974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-29.9 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.580, 82.594, 139.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Adenylyl-sulfate kinase / APS kinase / Adenosine-5'-phosphosulfate kinase / ATP adenosine-5'-phosphosulfate 3'-phosphotransferase


Mass: 22354.123 Da / Num. of mol.: 4 / Fragment: UNP residues 23-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Strain: ATTC 24791 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12657, adenylyl-sulfate kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE


Mass: 507.264 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O13P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: bis tris, PEG 3350, ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9194 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2007 / Details: Double-crystal monochromator
RadiationMonochromator: Double Si(111) crystal, paralell / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.5→31.718 Å / Num. all: 31582 / Num. obs: 31427 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 1.5 / Num. measured all: 8337 / Num. unique all: 2290 / Rsym value: 0.486 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Translation4 Å1000 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
EPMRphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly alanine model of pdb entry 1M7G A chain

1m7g


Resolution: 2.5→31.715 Å / Isotropic thermal model: isotropic / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2278 4.11 %random
Rwork0.198 ---
all0.202 ---
obs0.201 31427 92.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 0 Å2 / Biso mean: 37.49 Å2 / Biso min: 391.05 Å2
Baniso -1Baniso -2Baniso -3
1--5.379 Å2-0 Å20 Å2
2---2.823 Å20 Å2
3---7.393 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 173 495 6230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015847
X-RAY DIFFRACTIONf_angle_d1.4217981
X-RAY DIFFRACTIONf_chiral_restr0.073890
X-RAY DIFFRACTIONf_plane_restr0.0071020
X-RAY DIFFRACTIONf_dihedral_angle_d22.262153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5540.3861430.2962931307483
2.554-2.6140.3931110.2742999311084
2.614-2.6790.2891130.2573155326886
2.679-2.7510.2981520.2413144329689
2.751-2.8320.3751350.243251338690
2.832-2.9240.3071170.2453256337392
2.924-3.0280.3391320.2373372350493
3.028-3.1490.3411450.2183390353595
3.149-3.2930.2681480.2083446359497
3.293-3.4660.2731640.1963446361097
3.466-3.6830.2851420.1683486362897
3.683-3.9670.2661610.1343477363897
3.967-4.3650.1711640.1253480364498
4.365-4.9940.2171640.123443360797
4.994-6.2840.2191560.1643426358296
6.284-31.7180.2661310.1993416354795

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