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- PDB-1m15: Transition state structure of arginine kinase -

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Basic information

Entry
Database: PDB / ID: 1m15
TitleTransition state structure of arginine kinase
Componentsarginine kinase
KeywordsTRANSFERASE / ARGININE KINASE / CREATINE KINASE / PHOSPHAGEN KINASE / TRANSITION STATE ANALOG / ADENOSINE TRIPHOSPHATE
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 / ARGININE / NITRATE ION / Arginine kinase
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsYousef, M.S. / Fabiola, F. / Gattis, J.L. / Somasundaram, T. / Chapman, M.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights.
Authors: Yousef, M.S. / Fabiola, F. / Gattis, J.L. / Somasundaram, T. / Chapman, M.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Critical Initial Real-Space Refinement in the 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.
#3: 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.
History
DepositionJun 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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

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Assembly

Deposited unit
A: arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0006
Polymers40,2501
Non-polymers7515
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.393, 70.312, 80.319
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 / AK


Mass: 40249.758 Da / Num. of mol.: 1 / Mutation: E103Q, D112G, G116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limulus polyphemus (Atlantic horseshoe crab)
Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: P51541, arginine kinase

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Non-polymers , 5 types, 562 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-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 1.98 Å3/Da / Density % sol: 46.36 %
Crystal growpH: 8 / Details: pH 8
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Zhou, G., (1997) Protein Sci., 6, 444.
Components of the solutions
*PLUS
Conc.: 15-20 % / Common name: PEG6000 / Details: pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 1999
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 115910 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Rsym value: 0.048 / Net I/σ(I): 24
Reflection shellResolution: 1.2→1.23 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.323 / % possible all: 71.5
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 1112071 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 1.2 Å / % possible obs: 71.5 % / Rmerge(I) obs: 0.323

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Processing

Software
NameVersionClassification
SHELXL-97refinement
SCALEPACKSUITE (DENZOdata scaling
XDISPLAYF)data collection
CNSrefinement
SHELXmodel building
DENZOSUITE (DENZOdata reduction
XDISPLAYF)data reduction
CNSphasing
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BGO

1bgo


Resolution: 1.2→6 Å / Num. parameters: 31135 / Num. restraintsaints: 37290 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4%
RfactorNum. reflection% reflectionSelection details
Rfree0.1395 6 -RANDOM
Rwork0.1248 ---
all0.1248 102470 --
obs0.127 -90 %-
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 2820 / Occupancy sum non hydrogen: 3422
Refinement stepCycle: LAST / Resolution: 1.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 48 557 3459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0303
X-RAY DIFFRACTIONs_zero_chiral_vol0.249
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.119
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.226
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0.098
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 6 Å / Num. reflection Rfree: 3074 / Rfactor Rfree: 0.1225 / Rfactor Rwork: 0.1082
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.33
LS refinement shell
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 1.24 Å / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.214

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