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- PDB-4ix4: Crystal structure of a Stt7 homolog from Micromonas algae in comp... -

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Basic information

Entry
Database: PDB / ID: 4ix4
TitleCrystal structure of a Stt7 homolog from Micromonas algae in complex with ADP
ComponentsMsStt7d protein
KeywordsTRANSFERASE / protein kinase / canonical protein kinase fold / ATP binding
Function / homology
Function and homology information


protein kinase activity / ATP binding / metal ion binding
Similarity search - Function
PDZ superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...PDZ superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein kinase domain-containing protein
Similarity search - Component
Biological speciesMicromonas (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 1.499 Å
AuthorsGuo, J. / Wei, X. / Li, M. / Pan, X. / Chang, W. / Liu, Z.
CitationJournal: Protein Cell / Year: 2013
Title: Structure of the catalytic domain of a state transition kinase homolog from Micromonas algae
Authors: Guo, J. / Wei, X. / Li, M. / Pan, X. / Chang, W. / Liu, Z.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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: MsStt7d protein
B: MsStt7d protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3937
Polymers75,4662
Non-polymers9275
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-45 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.930, 133.027, 55.155
Angle α, β, γ (deg.)90.00, 116.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MsStt7d protein


Mass: 37732.906 Da / Num. of mol.: 2 / Fragment: UNP residues 151-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonas (plant) / Strain: RCC299 / Gene: STT7 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C1EBN1
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 200mM MgCl2, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97854 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.499→50 Å / Num. all: 110939 / Num. obs: 110828 / % possible obs: 99.9 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.063 / Net I/σ(I): 32.88
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 5510 / Rsym value: 0.542 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: Difference Fourier / Resolution: 1.499→39.641 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 18.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1988 5412 5.01 %RANDOM
Rwork0.1566 ---
all0.163 110930 --
obs0.1587 108035 97.39 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.91 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4699 Å20 Å2-1.954 Å2
2---2.006 Å2-0 Å2
3---1.5361 Å2
Refinement stepCycle: LAST / Resolution: 1.499→39.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 57 654 5957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055461
X-RAY DIFFRACTIONf_angle_d1.0197414
X-RAY DIFFRACTIONf_dihedral_angle_d14.9582010
X-RAY DIFFRACTIONf_chiral_restr0.066798
X-RAY DIFFRACTIONf_plane_restr0.004978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4995-1.55310.2175000.1474964292
1.5531-1.61530.20295170.1255990094
1.6153-1.68880.18435430.11731012996
1.6888-1.77780.17955400.11671020097
1.7778-1.88920.20525380.12781028398
1.8892-2.0350.19055560.13591039899
2.035-2.23980.19265450.1451044899
2.2398-2.56390.19915460.158610528100
2.5639-3.230.22596080.188310492100
3.23-39.65490.18665190.16821060399

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