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- PDB-4gw0: Crystal structure of arginine kinase in complex with imino-L-orni... -

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Basic information

Entry
Database: PDB / ID: 4gw0
TitleCrystal structure of arginine kinase in complex with imino-L-ornithine, MgADP, and nitrate.
ComponentsArginine kinase
KeywordsTRANSFERASE / Arginine kinase / Phosphagen kinase / Transition state analog / Kinase
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 / N5-IMINOETHYL-L-ORNITHINE / NITRATE ION / Arginine kinase
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.448 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 1.2Sep 13, 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 / 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

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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)40,9365
Polymers40,2501
Non-polymers6874
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.184, 71.103, 79.962
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, 186 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-ILO / N5-IMINOETHYL-L-ORNITHINE


Mass: 173.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15N3O2
#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.: 182 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
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 298.0K

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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: 2.448→32.485 Å / Num. all: 13808 / Num. obs: 13808 / % possible obs: 97.17 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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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: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M15

1m15


Resolution: 2.448→32.485 Å / SU ML: 0.27 / σ(F): 1 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.21 406 2.94 %Used same test set as PDB entry 1M15
Rwork0.1782 ---
obs0.1792 13808 97.17 %-
all-13808 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.014 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.394 Å20 Å2-0 Å2
2--13.7961 Å2-0 Å2
3----7.4022 Å2
Refinement stepCycle: LAST / Resolution: 2.448→32.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 44 182 3043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072964
X-RAY DIFFRACTIONf_angle_d0.8334003
X-RAY DIFFRACTIONf_dihedral_angle_d14.5621122
X-RAY DIFFRACTIONf_chiral_restr0.058438
X-RAY DIFFRACTIONf_plane_restr0.004511
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6602-0.50280.37692.2831-0.06842.36060.008-0.1910.46220.0734-0.01590.6421-0.8152-0.9373-0.04420.24110.14750.00730.1462-0.0640.2522-3.68974.1368-0.5216
21.16780.49080.24911.4187-0.30761.22740.11060.52930.0499-0.28980.0264-0.014-0.04690.12260.0180.20380.0203-0.02030.1802-0.01880.10798.6224-7.2677-17.0193
30.1320.10430.1870.320.32910.40330.52390.2441-0.5067-0.3038-0.14830.10110.6682-0.05550.18720.3990.0831-0.16360.1198-0.14530.25459.196-23.5182-9.1281
41.54020.04630.23311.2996-0.4961.59740.14430.1203-0.13830.1883-0.4042-0.2575-0.16930.6027-0.1070.0753-0.0584-0.02770.09510.00170.090321.1317-8.66061.5439
50.8366-0.38390.53061.06720.00750.52190.0778-0.43950.07230.6585-0.03830.5064-0.1113-0.16840.01150.2117-0.05410.04270.1883-0.00130.21379.6207-10.591712.8332
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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