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- PDB-1nks: ADENYLATE KINASE FROM SULFOLOBUS ACIDOCALDARIUS -

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Basic information

Entry
Database: PDB / ID: 1nks
TitleADENYLATE KINASE FROM SULFOLOBUS ACIDOCALDARIUS
ComponentsADENYLATE KINASE
KeywordsKINASE / THERMOPHILIC / TRANSFERASE
Function / homology
Function and homology information


adenylate kinase / AMP kinase activity / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase AdkA / AAA domain / 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 / ADENOSINE MONOPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.57 Å
AuthorsVonrhein, C. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The structure of a trimeric archaeal adenylate kinase.
Authors: Vonrhein, C. / Bonisch, H. / Schafer, G. / Schulz, G.E.
History
DepositionJul 16, 1998Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: ADENYLATE KINASE
B: ADENYLATE KINASE
C: ADENYLATE KINASE
D: ADENYLATE KINASE
E: ADENYLATE KINASE
F: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,29310
Polymers126,8246
Non-polymers1,4694
Water5,981332
1
A: ADENYLATE KINASE
B: ADENYLATE KINASE
C: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7594
Polymers63,4123
Non-polymers3471
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-30 kcal/mol
Surface area24910 Å2
MethodPISA
2
D: ADENYLATE KINASE
E: ADENYLATE KINASE
F: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5346
Polymers63,4123
Non-polymers1,1223
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-35 kcal/mol
Surface area23880 Å2
MethodPISA
3
D: ADENYLATE KINASE
E: ADENYLATE KINASE
F: ADENYLATE KINASE
hetero molecules

A: ADENYLATE KINASE
B: ADENYLATE KINASE
C: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,29310
Polymers126,8246
Non-polymers1,4694
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area13140 Å2
ΔGint-70 kcal/mol
Surface area47300 Å2
MethodPISA
4
D: ADENYLATE KINASE
E: ADENYLATE KINASE
F: ADENYLATE KINASE
hetero molecules

A: ADENYLATE KINASE
B: ADENYLATE KINASE
C: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,29310
Polymers126,8246
Non-polymers1,4694
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y+1/2,-z+3/21
Buried area12680 Å2
ΔGint-69 kcal/mol
Surface area47760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.510, 145.690, 172.280
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
ADENYLATE KINASE / ATP\:AMP PHOSPHOTRANSFERASE


Mass: 21137.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Plasmid: PET3A / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P35028, adenylate kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66 %
Description: LOW RESOLUTION DATA WERE COLLECTED ON A ROTATING ANODE AND MERGED WITH HIGH-RESOLUTION DATA COLLECTED FROM THE SYNCHROTRON SOURCE DESCRIBED ABOVE.
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 2 M SODIUM FORMATE AT PH 7.5 AT A PROTEIN CONCENTRATION OF 5 MG/ML; PROTEIN SOLUTION WAS QUARTZ-DISTILLED AND NO NUCLEOTIDES WERE ADDED.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
22 Msodium formate1drop
34 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9123
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: DUAL SLITS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9123 Å / Relative weight: 1
ReflectionResolution: 2.57→40 Å / Num. obs: 54962 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.091 / Net I/σ(I): 13.3
Reflection shellResolution: 2.57→2.64 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.266 / % possible all: 56
Reflection
*PLUS
Num. measured all: 168355 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 56 % / Rmerge(I) obs: 0.266

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Processing

Software
NameVersionClassification
MLPHAREphasing
GETAXmodel building
DMmodel building
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
GETAXphasing
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.57→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT CORRECTION AS IMPLEMENTED IN X-PLOR 3.851 WAS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 -2 %RANDOM
Rwork0.164 ---
obs-54962 92 %-
Refinement stepCycle: LAST / Resolution: 2.57→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8904 0 96 332 9332
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164
Solvent computation
*PLUS
Displacement parameters
*PLUS

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