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- PDB-5u8e: Crystal Structure of substrate-free arginine kinase from spider P... -

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Basic information

Entry
Database: PDB / ID: 5u8e
TitleCrystal Structure of substrate-free arginine kinase from spider Polybetes pythagoricus
Componentsarginine kinase
KeywordsTRANSFERASE / phosphagen metabolism / arginine kinase / spider / open conformation / free-ligand
Function / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding
Similarity search - Function
Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain ...Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPolybetes pythagoricus (spider)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsLopez-Zavala, A.A. / Garcia, C.F. / Hernadez-Paredes, J. / Sotelo-Mundo, R.R.
Funding support Mexico, Argentina, 4items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y TecnologiaINFR-2014-01-225455 Mexico
Consejo Nacional de Ciencia y TecnologiaC0005-2012-189333 Mexico
National Scientific and Technical Research Council (CONICET)COOP-CTES-D680 Argentina
ANPC PICT2014-2580 Argentina
CitationJournal: PeerJ / Year: 2017
Title: Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus.
Authors: Laino, A. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Carrasco-Miranda, J.S. / Santana, M. / Stojanoff, V. / Sotelo-Mundo, R.R. / Garcia, C.F.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 4, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3142
Polymers43,2911
Non-polymers231
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-9 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.131, 61.117, 60.991
Angle α, β, γ (deg.)90.00, 95.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein arginine kinase /


Mass: 43291.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: two loops were found disordered and Cys was oxidized form
Source: (gene. exp.) Polybetes pythagoricus (spider) / Plasmid: pjexpress414 / Details (production host): T7 promoterB, Ampr, pUC originC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: A0A286R7K5*PLUS, arginine kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.23 Å3/Da / Density % sol: 40.33 % / Description: large-thin plates, colorless
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% w/v polyethylene glycol 4000.
Temp details: none

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54178 Å
DetectorType: BRUKER PHOTON 100 / Detector: PIXEL / Date: Apr 27, 2016 / Details: quazar multilayer
RadiationMonochromator: sealed tube/flat / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.18→20.3 Å / Num. obs: 18342 / % possible obs: 99.43 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.38 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.0476 / Rsym value: 0.0847 / Net I/σ(I): 24.7
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3.34 / CC1/2: 0.739 / % possible all: 94.27

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PROTEUM PLUSv2data reduction
PROTEUM PLUSV2data scaling
PHASER2.1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AM1

4am1


Resolution: 2.18→20.307 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 968 5.28 %random selection
Rwork0.1724 ---
obs0.1752 18342 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→20.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 1 266 2979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072767
X-RAY DIFFRACTIONf_angle_d0.8523740
X-RAY DIFFRACTIONf_dihedral_angle_d7.2971668
X-RAY DIFFRACTIONf_chiral_restr0.05414
X-RAY DIFFRACTIONf_plane_restr0.006487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1799-2.29470.29481210.22962375X-RAY DIFFRACTION96
2.2947-2.43830.27991520.20732482X-RAY DIFFRACTION100
2.4383-2.62620.27631360.19482467X-RAY DIFFRACTION100
2.6262-2.88980.23251420.18692484X-RAY DIFFRACTION100
2.8898-3.30640.191360.17112488X-RAY DIFFRACTION100
3.3064-4.15980.21721460.14312508X-RAY DIFFRACTION100
4.1598-20.30820.19121350.15432570X-RAY DIFFRACTION100

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