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- PDB-2eu8: Crystal structure of a thermostable mutant of Bacillus subtilis A... -

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Basic information

Entry
Database: PDB / ID: 2eu8
TitleCrystal structure of a thermostable mutant of Bacillus subtilis Adenylate Kinase (Q199R)
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Adenylate kinase / thermostability / point mutant / in vivo evolution
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity ...nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / zinc ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP 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
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, S. / Shamoo, Y.
CitationJournal: Mol.Cell / Year: 2006
Title: In vivo molecular evolution reveals biophysical origins of organismal fitness.
Authors: Counago, R. / Chen, S. / Shamoo, Y.
History
DepositionOct 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1479
Polymers48,0952
Non-polymers2,0527
Water11,836657
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0534
Polymers24,0471
Non-polymers1,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0935
Polymers24,0471
Non-polymers1,0464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.690, 75.140, 77.350
Angle α, β, γ (deg.)90.00, 98.13, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenylate kinase / ATP-AMP transphosphorylase / AK / Superoxide-inducible protein 16 / SOI16


Mass: 24047.285 Da / Num. of mol.: 2 / Mutation: Q199R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: adk / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16304, adenylate kinase

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Non-polymers , 5 types, 664 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.063 Å3/Da / Density % sol: 38.07 %
Crystal growTemperature: 293.14 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.75mM protein, PEG1500, Calcium Chloride, Ches, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.14K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2005
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→37.57 Å / Num. all: 48747 / Num. obs: 48747 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.84 % / Rmerge(I) obs: 0.036 / Χ2: 0.89 / Net I/σ(I): 21.7 / Scaling rejects: 1416
Reflection shellResolution: 1.6→1.66 Å / % possible obs: 80.4 % / Redundancy: 3.47 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 8.7 / Num. measured obs: 122 / Num. unique all: 4179 / Χ2: 0.77 / % possible all: 80.4

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.544 / Packing: 0.557
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation3 Å15 Ågeneral98.4 0

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZIN

1zin


Resolution: 1.8→37.57 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1747 4.8 %RANDOM
Rwork0.187 ---
all0.19 36475 --
obs0.2289 35105 96.2 %-
Solvent computationBsol: 34.988 Å2
Displacement parametersBiso mean: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.659 Å20 Å2-1.769 Å2
2---0.313 Å20 Å2
3---0.972 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.232 Å0.1917 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1429 Å0.0784 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 119 657 4142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004967
X-RAY DIFFRACTIONc_angle_deg1.23454
X-RAY DIFFRACTIONc_dihedral_angle_d20.40305
X-RAY DIFFRACTIONc_improper_angle_d0.87924
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.2513 176 -
Rwork0.201 --
obs-3189 0.8856 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3ap5_xplor_par.txt
X-RAY DIFFRACTION4water_rep.param

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