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- PDB-3ju6: Crystal Structure of Dimeric Arginine Kinase in Complex with AMPP... -

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Basic information

Entry
Database: PDB / ID: 3ju6
TitleCrystal Structure of Dimeric Arginine Kinase in Complex with AMPPNP and Arginine
ComponentsArginine kinase
KeywordsTRANSFERASE / Arginine Kinase / Reciprocating Mechanism / Negative Cooperativity / Phosphagen Kinase / Ternary Complex / ATP-binding / Kinase / Nucleotide-binding
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ARGININE / Arginine kinase
Similarity search - Component
Biological speciesApostichopus japonicus (Japanese sea cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWu, X. / Ye, S. / Guo, S. / Yan, W. / Bartlam, M. / Rao, Z.
CitationJournal: Faseb J. / Year: 2010
Title: Structural basis for a reciprocating mechanism of negative cooperativity in dimeric phosphagen kinase activity
Authors: Wu, X. / Ye, S. / Guo, S. / Yan, W. / Bartlam, M. / Rao, Z.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 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
B: Arginine kinase
C: Arginine kinase
D: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,7716
Polymers171,0904
Non-polymers6812
Water31,7601763
1
A: Arginine kinase
B: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2264
Polymers85,5452
Non-polymers6812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint1 kcal/mol
Surface area30080 Å2
MethodPISA
2
C: Arginine kinase
D: Arginine kinase


Theoretical massNumber of molelcules
Total (without water)85,5452
Polymers85,5452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint0 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.823, 60.073, 139.946
Angle α, β, γ (deg.)90.00, 93.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Arginine kinase / / AK


Mass: 42772.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apostichopus japonicus (Japanese sea cucumber)
Gene: AK / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9XY07, arginine kinase
#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1763 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M Bis-Tris (pH 6.6), 12% PEG 1000, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9786 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 53651 / Num. obs: 52310 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 22.8
Reflection shellResolution: 2.45→2.52 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 14.3 / Num. unique all: 4434 / % possible all: 89.7

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JU5

3ju5


Resolution: 2.45→47.01 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 5244 9.8 %random
Rwork0.214 ---
all0.225 53651 --
obs0.223 51928 97.5 %-
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.698 Å20 Å2-4.792 Å2
2--1.36 Å20 Å2
3----0.662 Å2
Refinement stepCycle: LAST / Resolution: 2.45→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11544 0 43 1763 13350
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_bond_d0.0092
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.33
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.302 461 8.7 %
Rwork0.243 4241 -
obs--88.9 %

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