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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 / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding / cytoplasm
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
ADENOSINE-5'-DIPHOSPHATE / D-ARGININE / NITRATE ION / Arginine kinase
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / molecular replacement, MIR / Resolution: 1.86 Å
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.
History
DepositionJun 3, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_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.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.value / _struct_conn.pdbx_dist_value / _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.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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGININE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8696
Polymers40,1191
Non-polymers7515
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ARGININE KINASE


Mass: 40118.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab)
Tissue: MUSCLE / Cellular location: CYTOPLASM / Gene: AK17 / Plasmid: PET-22B / 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 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-DAR / D-ARGININE


Type: D-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.24 Å3/Da / Density % 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
*PLUS
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 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 13, 1996 / Details: GRAPHITE MONOCHROMATOR OPTICS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→35 Å / Num. obs: 34737 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.9
Reflection shellResolution: 1.86→1.94 Å / Rmerge(I) obs: 0.157 / % possible all: 98.5
Reflection shell
*PLUS
% 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
RefinementMethod to determine structure: molecular replacement, MIR
Starting model: 1CRK, MITOCHONDRIAL CREATINE KINASE

1crk


Resolution: 1.86→5 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0.01 / Isotropic thermal model: GAUSSIAN DISTRIBUTION / Cross valid method: THROUGHOUT / σ(F): 2
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)).
RfactorNum. reflection% reflectionSelection details
Rfree0.224 -3 %RANDOM
Rwork0.196 ---
obs0.196 29223 98.9 %-
Displacement parametersBiso mean: 16.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.237 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.86→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 51 298 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_d22.4
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_it1.83
X-RAY DIFFRACTIONx_scangle_it2.803
LS refinement shellResolution: 1.86→1.94 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.255 -3 %
Rwork0.236 3314 -
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_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15

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