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- PDB-4gvy: Crystal structure of arginine kinase in complex with L-citrulline... -

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Basic information

Entry
Database: PDB / ID: 4gvy
TitleCrystal structure of arginine kinase in complex with L-citrulline and MgADP
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 / extracellular space / 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 / CITRULLINE / Arginine kinase
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH PDB ENTRY 1M15 / Resolution: 2.091 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.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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8764
Polymers40,2501
Non-polymers6273
Water4,648258
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

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-CIR / CITRULLINE


Type: L-peptide linking / Mass: 175.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13N3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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 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: 2.091→17.635 Å / Num. all: 20717 / Num. obs: 20717 / % possible obs: 92.14 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.091→2.252 Å / % possible all: 81

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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

1m15


Resolution: 2.091→17.635 Å / SU ML: 0.21 / σ(F): 1 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 636 3.07 %Used same test set as PDB entry 1M15
Rwork0.175 ---
obs0.1761 20717 92.14 %-
all-20717 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.164 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.2654 Å20 Å2-0 Å2
2--15.1452 Å2-0 Å2
3----6.8797 Å2
Refinement stepCycle: LAST / Resolution: 2.091→17.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 40 258 3115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062970
X-RAY DIFFRACTIONf_angle_d0.9754013
X-RAY DIFFRACTIONf_dihedral_angle_d14.371127
X-RAY DIFFRACTIONf_chiral_restr0.067439
X-RAY DIFFRACTIONf_plane_restr0.006512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0906-2.25170.25251150.21923460X-RAY DIFFRACTION81
2.2517-2.47770.25231270.20073895X-RAY DIFFRACTION91
2.4777-2.8350.25941230.19924064X-RAY DIFFRACTION94
2.835-3.56690.22891370.18624218X-RAY DIFFRACTION97
3.5669-17.63540.16421340.14694444X-RAY DIFFRACTION98
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)
11.7131-0.238-0.35332.58760.17272.32660.004-0.2299-0.4490.0955-0.037-0.71120.75790.8384-0.04340.34250.1594-0.01080.27280.09390.34736.4448-4.054939.6727
21.04560.8885-0.4011.11930.05251.58060.03620.57130.0353-0.23820.08150.00480.1376-0.19620.0030.24860.00240.00230.26040.03060.185824.11927.265723.0947
30.05250.0701-0.02130.1237-0.16660.71090.40040.23770.56010.0738-0.1638-0.1625-0.78320.0480.13680.47920.09470.21910.12640.20640.45223.479723.529431.1156
42.1150.1629-0.36691.42340.77172.25110.11340.12390.15180.1615-0.26480.16590.2189-0.5963-0.02580.1775-0.05010.01150.21760.00110.198911.57318.60741.693
50.5382-0.3109-0.25090.7541-0.21160.34820.0708-0.44060.14270.7007-0.0418-0.3958-0.08680.25520.00840.2849-0.0605-0.03110.2387-0.00420.222722.97669.897752.9396
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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