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- PDB-4gw2: Crystal structure of arginine kinase in complex with L-ornithine,... -

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Basic information

Entry
Database: PDB / ID: 4gw2
TitleCrystal structure of arginine kinase in complex with L-ornithine, MgADP, and nitrate.
ComponentsArginine kinase
KeywordsTRANSFERASE / Arginine kinase / Phosphagen kinase / Transition state analog / Kinase
Function / homology
Function and homology information


arginine kinase activity / arginine kinase / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
ATP:guanido phosphotransferase, N-terminal domain / Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / Phosphagen kinase C-terminal domain profile. / ATP:guanido phosphotransferase, C-terminal catalytic domain ...ATP:guanido phosphotransferase, N-terminal domain / Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / Phosphagen kinase C-terminal domain profile. / ATP:guanido phosphotransferase, C-terminal catalytic domain / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase / 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 / NITRATE ION / L-ornithine / Arginine kinase
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH PDB ENTRY 1M15 / Resolution: 2.157 Å
AuthorsClark, S.A. / Davulcu, O. / Chapman, M.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs.
Authors: Clark, S.A. / Davulcu, O. / Chapman, M.S.
History
DepositionAug 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.3Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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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)40,8955
Polymers40,2501
Non-polymers6464
Water4,306239
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: E103N, 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, 243 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 398.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.541 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.157→29.648 Å / Num. all: 19862 / Num. obs: 19862 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.157→2.374 Å / % possible all: 91

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH PDB ENTRY 1M15
Starting model: PDB ENTRY 1M15
Resolution: 2.157→29.648 Å / SU ML: 0.3 / σ(F): 1 / σ(I): 1 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 600 3.02 %Used same test set as PDB entry 1M15
Rwork0.1934 ---
obs0.1944 19862 96.7 %-
all-19862 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.772 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.701 Å20 Å2-0 Å2
2--13.4519 Å2-0 Å2
3----6.7508 Å2
Refinement stepCycle: LAST / Resolution: 2.157→29.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 41 239 3097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062963
X-RAY DIFFRACTIONf_angle_d0.8924001
X-RAY DIFFRACTIONf_dihedral_angle_d14.0991121
X-RAY DIFFRACTIONf_chiral_restr0.065438
X-RAY DIFFRACTIONf_plane_restr0.005510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1569-2.37380.31841430.24734448X-RAY DIFFRACTION91
2.3738-2.71710.27831460.22574761X-RAY DIFFRACTION97
2.7171-3.42250.21861540.20444915X-RAY DIFFRACTION99
3.4225-29.65050.19821570.16755138X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.10010.0457-0.17351.7675-0.28231.9733-0.0907-0.3273-0.7328-0.0516-0.1462-0.73150.75860.9023-0.2310.33970.31980.05080.33890.27120.390436.3705-4.448339.7073
21.49580.6236-0.56370.94990.21641.94250.03460.51170.0438-0.31480.0610.02710.2324-0.0278-0.00010.2632-0.0227-0.01560.25610.01080.206724.38377.171523.1503
31.2775-0.0113-0.54290.00060.00470.23080.53620.26990.7598-0.2981-0.0539-0.1981-0.7944-0.00490.29170.45270.00780.17480.11780.07270.467324.035423.452131.0868
42.39310.1802-0.67360.9040.61162.38510.07350.03410.11750.1008-0.13370.19210.2196-0.4203-0.05970.1433-0.05180.00580.10840.03270.165511.58988.729741.6374
50.5642-0.3426-0.20090.3872-0.10840.37090.1-0.4948-0.06650.5599-0.0473-0.3864-0.03940.322600.3346-0.0895-0.02950.36650.04080.267623.12910.339253.1243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:102 OR RESID 193:201 OR RESID 269:276 ) )A2 - 102
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:102 OR RESID 193:201 OR RESID 269:276 ) )A193 - 201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:102 OR RESID 193:201 OR RESID 269:276 ) )A269 - 276
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 129:155 OR RESID 167:173 OR RESID 202:213 OR RESID 221:229 OR RESID 258:259 ) )A129 - 155
5X-RAY DIFFRACTION2( CHAIN A AND ( RESID 129:155 OR RESID 167:173 OR RESID 202:213 OR RESID 221:229 OR RESID 258:259 ) )A167 - 173
6X-RAY DIFFRACTION2( CHAIN A AND ( RESID 129:155 OR RESID 167:173 OR RESID 202:213 OR RESID 221:229 OR RESID 258:259 ) )A202 - 213
7X-RAY DIFFRACTION2( CHAIN A AND ( RESID 129:155 OR RESID 167:173 OR RESID 202:213 OR RESID 221:229 OR RESID 258:259 ) )A221 - 229
8X-RAY DIFFRACTION2( CHAIN A AND ( RESID 129:155 OR RESID 167:173 OR RESID 202:213 OR RESID 221:229 OR RESID 258:259 ) )A258 - 259
9X-RAY DIFFRACTION3( CHAIN A AND RESID 174:187 )A174 - 187
10X-RAY DIFFRACTION4( CHAIN A AND ( RESID 103:128 OR RESID 156:166 OR RESID 216:220 OR RESID 233:257 OR RESID 260:268 OR RESID 277:290 OR RESID 330:357 ) )A103 - 128
11X-RAY DIFFRACTION4( CHAIN A AND ( RESID 103:128 OR RESID 156:166 OR RESID 216:220 OR RESID 233:257 OR RESID 260:268 OR RESID 277:290 OR RESID 330:357 ) )A156 - 166
12X-RAY DIFFRACTION4( CHAIN A AND ( RESID 103:128 OR RESID 156:166 OR RESID 216:220 OR RESID 233:257 OR RESID 260:268 OR RESID 277:290 OR RESID 330:357 ) )A216 - 220
13X-RAY DIFFRACTION4( CHAIN A AND ( RESID 103:128 OR RESID 156:166 OR RESID 216:220 OR RESID 233:257 OR RESID 260:268 OR RESID 277:290 OR RESID 330:357 ) )A233 - 257
14X-RAY DIFFRACTION4( CHAIN A AND ( RESID 103:128 OR RESID 156:166 OR RESID 216:220 OR RESID 233:257 OR RESID 260:268 OR RESID 277:290 OR RESID 330:357 ) )A260 - 268
15X-RAY DIFFRACTION4( CHAIN A AND ( RESID 103:128 OR RESID 156:166 OR RESID 216:220 OR RESID 233:257 OR RESID 260:268 OR RESID 277:290 OR RESID 330:357 ) )A277 - 290
16X-RAY DIFFRACTION4( CHAIN A AND ( RESID 103:128 OR RESID 156:166 OR RESID 216:220 OR RESID 233:257 OR RESID 260:268 OR RESID 277:290 OR RESID 330:357 ) )A330 - 357
17X-RAY DIFFRACTION5( CHAIN A AND ( RESID 293:310 OR RESID 321:329 ) )A293 - 310
18X-RAY DIFFRACTION5( CHAIN A AND ( RESID 293:310 OR RESID 321:329 ) )A321 - 329

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