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- PDB-1bg0: TRANSITION STATE STRUCTURE OF ARGININE KINASE -

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Basic information

Entry
Database: PDB / ID: 1bg0
TitleTRANSITION STATE STRUCTURE OF ARGININE KINASE
ComponentsARGININE KINASE
KeywordsKINASE / ARGININE KINASE / CREATINE KINASE / PHOSPHAGEN KINASE / TRANSITION STATE ANALOG / ADENOSINE TRIPHOSPHATE / TRANSFERASE
Function / homologyATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Phosphagen kinase N-terminal domain profile. / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / Glutamine synthetase/guanido kinase, catalytic domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase active site ...ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Phosphagen kinase N-terminal domain profile. / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / Glutamine synthetase/guanido kinase, catalytic domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase active site / ATP:guanido phosphotransferase, N-terminal domain superfamily / arginine kinase / arginine kinase activity / phosphorylation / ATP binding / cytoplasm / Arginine kinase
Function and homology information
Specimen sourceLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / molecular replacement, MIR / 1.86 Å resolution
AuthorsZhou, G. / Somasundaram, T. / Blanc, E. / Parthasarathy, G. / Ellington, W.R. / Chapman, M.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions.
Authors: Zhou, G. / Somasundaram, T. / Blanc, E. / Parthasarathy, G. / Ellington, W.R. / Chapman, M.S.
#1: Journal: To be Published
Title: Critical Initial Real Space Refinement in Structure Determination of Arginine Kinase
Authors: Zhou, G. / Somasundaram, T. / Blanc, E. / Chen, Z. / Chapman, M.S.
#2: Journal: Protein Sci. / Year: 1997
Title: Expression, Purification from Inclusion Bodies, and Crystal Characterization of a Transition State Analog Complex of Arginine Kinase: A Model for Studying Phosphagen Kinases
Authors: Zhou, G. / Parthasarathy, G. / Somasundaram, T. / Ables, A. / Roy, L. / Strong, S.J. / Ellington, W.R. / Chapman, M.S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 3, 1998 / Release: Oct 14, 1998
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 14, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Mar 14, 2018Structure modelDatabase references / Otherpdbx_database_status / struct_ref_seq_dif_pdbx_database_status.process_site / _struct_ref_seq_dif.details

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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)40,8696
Polyers40,1191
Non-polymers7515
Water5,368298
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)65.439, 70.885, 80.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide ARGININE KINASE /


Mass: 40118.562 Da / Num. of mol.: 1
Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab)
Genus: Limulus / Tissue: MUSCLE / Cellular location: CYTOPLASM / Gene: AK17 / Plasmid name: PET-22B / Genus (production host): Escherichia / Gene (production host): AK17 / Production host: Escherichia coli (E. coli) / References: UniProt: P51541, arginine kinase

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Non-polymers , 5 types, 303 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Formula: NO3 / Nitrate
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Chemical ChemComp-DAR / D-ARGININE


Mass: 175.209 Da / Num. of mol.: 1 / Formula: C6H15N4O2 / Arginine
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Formula: H2O / Water

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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: 2.24 / Density percent sol: 45 %
Description: THE LARGE DOMAIN OF SUBUNIT A WAS USED AS A PROBE MODEL
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 6000, 53 MM MGCL2, 2MM MGADP-, 25 MM KNO3, 10 MM ARGININE 0.5 MM DTT, 2.5 MM SODIUM AZIDE, 25 MM HEPES, PH 7.5, WITH 20 MG/ML OF PROTEIN CONCENTRATION.
Crystal grow
*PLUS
Method: microdialysis / Details: Zhou, G., (1997) Protein Sci., 6, 444.
components of the solutions
*PLUS
Conc: 12 % / Common name: PEG6000 / Details: can be replaced by PEG1000

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Details: GRAPHITE MONOCHROMATOR OPTICS / Detector: IMAGE PLATE / Collection date: Sep 13, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 16.8 Å2 / D resolution high: 1.86 Å / D resolution low: 35 Å / Number obs: 34737 / Observed criterion sigma I: 1 / Rmerge I obs: 0.047 / NetI over sigmaI: 15.9 / Redundancy: 6.7 % / Percent possible obs: 98.9
Reflection shellRmerge I obs: 0.157 / Highest resolution: 1.86 Å / Lowest resolution: 1.94 Å / Percent possible all: 98.5
Reflection shell
*PLUS
Percent possible obs: 98.5

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefineMethod to determine structure: molecular replacement, MIR
Starting model: 1CRK, MITOCHONDRIAL CREATINE KINASE
Details: INITIAL LOW RESOLUTION REFINEMENT USED BOTH LOCAL REAL SPACE METHODS (CHAPMAN, M.S. ACTA CRYST., A51: 69-80 (1995); CHAPMAN, M.S. & BLANC, E. ACTA CRYST., 553: 203-6 (1997)).
R Free selection details: RANDOM / Data cutoff high absF: 10000 / Data cutoff low absF: 0.01 / Isotropic thermal model: GAUSSIAN DISTRIBUTION / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 16.6 Å2
Least-squares processR factor R free: 0.224 / R factor R work: 0.196 / R factor obs: 0.196 / Highest resolution: 1.86 Å / Lowest resolution: 5 Å / Number reflection obs: 29223 / Percent reflection R free: 3 / Percent reflection obs: 98.9
Refine analyzeLuzzati coordinate error free: 0.237 Å / Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.15 Å / Luzzati sigma a obs: 0.14 Å
Refine hist #LASTHighest resolution: 1.86 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 2816 / Nucleic acid: 0 / Ligand: 51 / Solvent: 298 / Total: 3165
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.40
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.945
X-RAY DIFFRACTIONx_mcangle_it1.449
X-RAY DIFFRACTIONx_scbond_it1.830
X-RAY DIFFRACTIONx_scangle_it2.803
Refine LS shellHighest resolution: 1.86 Å / R factor R free: 0.255 / R factor R work: 0.236 / Lowest resolution: 1.94 Å / Number reflection R work: 3314 / Total number of bins used: 8 / Percent reflection R free: 3 / Percent reflection obs: 98.5
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3ADP.PARADP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.40
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15

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