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- PDB-4rf6: Crystal structure of double-domain arginine kinase from Anthopleu... -

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Basic information

Entry
Database: PDB / ID: 4rf6
TitleCrystal structure of double-domain arginine kinase from Anthopleura japonicas
ComponentsArginine kinase
KeywordsTRANSFERASE / double domain / tandem domain / phosphagen kinase
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
Biological speciesAnthopleura japonica (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, Z. / Qiao, Z. / Ye, S. / Zhang, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.
Authors: Wang, Z. / Qiao, Z. / Ye, S. / Zhang, R.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginine kinase
B: Arginine kinase


Theoretical massNumber of molelcules
Total (without water)160,8852
Polymers160,8852
Non-polymers00
Water27,7071538
1
A: Arginine kinase


Theoretical massNumber of molelcules
Total (without water)80,4421
Polymers80,4421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arginine kinase


Theoretical massNumber of molelcules
Total (without water)80,4421
Polymers80,4421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.439, 58.913, 162.129
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arginine kinase / / AK


Mass: 80442.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anthopleura japonica (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: O15992, arginine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1538 / 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: 46.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.02M Tris, 0.05 NaCl, 0.005M MgCl2, 0.005M ADP, 0.1M Bis-Tris, 20% PEG5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.95→47.7 Å / Num. all: 107014 / Num. obs: 102413 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.95→1.99 Å / % possible all: 65.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JU5

3ju5


Resolution: 1.95→47.655 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.212 4687 5.04 %random
Rwork0.1724 ---
all0.176 107014 --
obs0.1745 93081 86.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→47.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11014 0 0 1538 12552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511299
X-RAY DIFFRACTIONf_angle_d0.93615251
X-RAY DIFFRACTIONf_dihedral_angle_d13.0654296
X-RAY DIFFRACTIONf_chiral_restr0.0581652
X-RAY DIFFRACTIONf_plane_restr0.0041989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.2914680.22631278X-RAY DIFFRACTION38
1.9722-1.99540.2334790.20791482X-RAY DIFFRACTION44
1.9954-2.01970.2758870.21694X-RAY DIFFRACTION50
2.0197-2.04530.28391010.21221875X-RAY DIFFRACTION56
2.0453-2.07220.24591060.20162045X-RAY DIFFRACTION61
2.0722-2.10060.22991270.19272353X-RAY DIFFRACTION70
2.1006-2.13060.23791380.19272547X-RAY DIFFRACTION77
2.1306-2.16240.22631330.19922751X-RAY DIFFRACTION80
2.1624-2.19620.24381320.19092763X-RAY DIFFRACTION83
2.1962-2.23220.2681470.18682866X-RAY DIFFRACTION85
2.2322-2.27070.20851850.18692991X-RAY DIFFRACTION88
2.2707-2.31190.22431690.18613001X-RAY DIFFRACTION91
2.3119-2.35640.23031720.18673152X-RAY DIFFRACTION93
2.3564-2.40450.23371510.19363224X-RAY DIFFRACTION96
2.4045-2.45680.26561790.18773352X-RAY DIFFRACTION98
2.4568-2.51390.23741880.18133338X-RAY DIFFRACTION99
2.5139-2.57680.27131840.1823400X-RAY DIFFRACTION100
2.5768-2.64650.21691690.17793340X-RAY DIFFRACTION100
2.6465-2.72430.22021940.17823360X-RAY DIFFRACTION100
2.7243-2.81230.2381560.17763414X-RAY DIFFRACTION100
2.8123-2.91280.21531960.1843337X-RAY DIFFRACTION100
2.9128-3.02940.22861720.1743410X-RAY DIFFRACTION100
3.0294-3.16720.21721940.16463332X-RAY DIFFRACTION100
3.1672-3.33420.18371900.16013408X-RAY DIFFRACTION100
3.3342-3.5430.16761780.15383409X-RAY DIFFRACTION100
3.543-3.81640.18361760.14943404X-RAY DIFFRACTION100
3.8164-4.20030.17891880.14343432X-RAY DIFFRACTION100
4.2003-4.80760.1731690.1413424X-RAY DIFFRACTION100
4.8076-6.05510.2251940.17633449X-RAY DIFFRACTION100
6.0551-47.6690.19731650.19063563X-RAY DIFFRACTION100
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)
11.1715-0.5095-0.22311.0439-0.37030.99760.07170.03790.1373-0.12310.0416-0.16930.12950.33940.00710.25540.07630.02630.3314-0.01510.232128.66579.0372-28.9774
20.1976-0.10710.25550.2293-0.09380.50210.035-0.1054-0.045-0.0060.12270.11060.2271-0.06320.10560.16220.004-0.00660.12620.00630.126515.92579.7613-5.5925
30.0069-0.02020.03030.0255-0.03760.06240.020.0312-0.0131-0.02790.1108-0.04890.2930.23350.30030.29580.4002-0.03620.1447-0.03360.145936.43093.6418.5566
40.2346-0.0102-0.00950.0678-0.02820.47080.07420.06530.119-0.058-0.105-0.1391-0.3136-0.0328-0.01310.15720.130.02760.11310.03130.144424.173926.84231.498
50.1493-0.0180.03550.31070.06310.4790.12460.0920.2248-0.2166-0.136-0.1571-0.3782-0.12270.01290.21520.06630.05790.09010.03230.253825.722537.549742.2675
60.273-0.1249-0.00220.3313-0.27580.4769-0.05390.02060.02160.0003-0.0169-0.09660.1143-0.0654-0.14870.0866-0.027-0.00490.0923-0.00490.08392.88728.9611122.0675
70.6533-0.1664-0.7511.1676-0.65381.540.0649-0.13320.18350.0027-0.0257-0.2338-0.29610.1969-0.0510.1749-0.00470.030.2215-0.01710.20112.551647.5057106.998
80.0984-0.0523-0.07280.26960.04720.5364-0.01340.00040.0260.08030.0366-0.16420.04660.06520.10460.07450.0253-0.03210.1026-0.00010.131621.203733.912476.3708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:63 )A0 - 63
2X-RAY DIFFRACTION2( CHAIN A AND RESID 64:290 )A64 - 290
3X-RAY DIFFRACTION3( CHAIN A AND RESID 291:405 )A291 - 405
4X-RAY DIFFRACTION4( CHAIN A AND RESID 406:578 )A406 - 578
5X-RAY DIFFRACTION5( CHAIN A AND RESID 579:714 )A579 - 714
6X-RAY DIFFRACTION6( CHAIN B AND RESID 0:290 )B0 - 290
7X-RAY DIFFRACTION7( CHAIN B AND RESID 291:340 )B291 - 340
8X-RAY DIFFRACTION8( CHAIN B AND RESID 341:713 )B341 - 713

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