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- PDB-3m10: Substrate-free form of Arginine Kinase -

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Basic information

Entry
Database: PDB / ID: 3m10
TitleSubstrate-free form of Arginine Kinase
ComponentsArginine kinase
KeywordsTRANSFERASE / Alpha-beta / ATP-binding / Kinase / Nucleotide-binding / Guanidino kinase / Phosphagen 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
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.727 Å
AuthorsYousef, M.S. / Clark, S.A. / Pruett, P.K. / Somasundaram, T. / Ellington, W.R. / Chapman, M.S.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility.
Authors: Niu, X. / Bruschweiler-Li, L. / Davulcu, O. / Skalicky, J.J. / Bruschweiler, R. / Chapman, M.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: De-icing: recovery of diffraction intensities in the presence of ice rings.
Authors: Chapman, M.S. / Somasundaram, T.
#2: Journal: Protein Sci. / Year: 2003
Title: Induced fit in guanidino kinases--comparison of substrate-free and transition state analog structures of arginine kinase.
Authors: Yousef, M.S. / Clark, S.A. / Pruett, P.K. / Somasundaram, T. / Ellington, W.R. / Chapman, M.S.
History
DepositionMar 3, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionMar 16, 2010ID: 1M80
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6924
Polymers80,5002
Non-polymers1922
Water17,294960
1
A: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3462
Polymers40,2501
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3462
Polymers40,2501
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.218, 90.428, 70.554
Angle α, β, γ (deg.)90.00, 111.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arginine kinase / / AK


Mass: 40249.758 Da / Num. of mol.: 2 / Mutation: E103Q, 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 960 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 mg/mL protein, 26% PEG5000 MME, 0.1M MES, 0.1M (NH4)2SO4. Small crystals were used for macroseeding identical conditions, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 2001 / Details: Bent conical Si Mirror (Rh-coated)
RadiationMonochromator: Bent Ge (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.727→28.513 Å / Num. all: 69678 / Num. obs: 65700 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 17.63 Å2 / Rsym value: 0.069 / Net I/σ(I): 11.69
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.11 / Rsym value: 0.517 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6_289)refinement
CNSrefinement
ADSCQuantumdata collection
Deice.py& DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M15

1m15


Resolution: 1.727→26.618 Å / SU ML: 0.23 / σ(F): 0.02 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 1866 2.9 %
Rwork0.1903 --
obs0.1918 64403 87.19 %
all-73865 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.1 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 28.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.4468 Å20 Å25.7777 Å2
2---9.3262 Å20 Å2
3---11.7729 Å2
Refine analyzeLuzzati sigma a free: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.727→26.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 10 960 6456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045676
X-RAY DIFFRACTIONf_angle_d0.8037664
X-RAY DIFFRACTIONf_dihedral_angle_d15.1982127
X-RAY DIFFRACTIONf_chiral_restr0.052838
X-RAY DIFFRACTIONf_plane_restr0.004996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7274-1.77410.29111400.25664153X-RAY DIFFRACTION76
1.7741-1.82630.31491350.24934448X-RAY DIFFRACTION82
1.8263-1.88520.28571220.24324425X-RAY DIFFRACTION80
1.8852-1.95260.36481400.31724379X-RAY DIFFRACTION80
1.9526-2.03070.2571370.2094879X-RAY DIFFRACTION89
2.0307-2.12310.23761590.19075104X-RAY DIFFRACTION92
2.1231-2.2350.23991370.18665010X-RAY DIFFRACTION91
2.235-2.37490.31011350.21164775X-RAY DIFFRACTION87
2.3749-2.55820.19991510.16865171X-RAY DIFFRACTION93
2.5582-2.81540.23781550.17255172X-RAY DIFFRACTION94
2.8154-3.22220.22881500.17855175X-RAY DIFFRACTION93
3.2222-4.05730.22221540.15665013X-RAY DIFFRACTION91
4.0573-26.62130.19291510.15794833X-RAY DIFFRACTION86
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)
10.5162-0.0426-0.15180.8004-0.17340.30860.1041-0.01880.2418-0.0612-0.009-0.1175-0.0908-0.01290.00260.12320.0111-0.00910.1474-0.03810.151921.256933.956651.3106
20.2033-0.5011-0.03611.79940.15880.09610.01050.0297-0.0712-0.0424-0.06460.22790.0443-0.0100.1098-0.012-0.01240.12480.00350.089620.21098.093546.2017
30.19820.0719-0.09090.1522-0.09360.8420.0109-0.05750.15630.39470.0209-0.3069-0.4526-0.0840.05010.2391-0.0557-0.11020.1440.00860.300544.78618.783457.0224
4-0.0105-0.0623-0.01440.0726-0.06190.0305-0.00140.06180.061-0.0293-0.1484-0.2328-0.1370.02790.00010.1242-0.0045-0.01860.16290.03580.227142.56168.003249.1642
50.65150.21630.08580.5923-0.11520.1257-0.05790.0286-0.4319-0.0032-0.0234-0.1920.01110.0128-0.00280.1227-0.00520.02730.1511-0.04060.210721.1302-6.379580.3139
60.82630.7733-0.03450.9868-0.0796-0.03910.0911-0.07590.16850.0748-0.0650.1434-0.0335-0.008300.1394-0.0080.02280.1187-0.01570.094519.777719.729685.0146
70.4656-0.0083-0.23260.1447-0.08160.2392-0.14770.339-0.4474-0.3029-0.0603-0.11140.2938-0.13970.00170.24890.03640.0860.17080.02280.262144.525718.591374.8941
80.14320.11190.21390.1257-0.05760.1829-0.0639-0.0654-0.2947-0.1638-0.0881-0.33160.14360.1013-0.00030.1608-0.00870.00710.16380.03490.213941.877219.729782.7339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 2:99
2X-RAY DIFFRACTION2chain A and resseq 100:280
3X-RAY DIFFRACTION3chain A and resseq 281:314
4X-RAY DIFFRACTION4chain A and resseq 315:357
5X-RAY DIFFRACTION5chain B and resseq 2:99
6X-RAY DIFFRACTION6chain B and resseq 100:280
7X-RAY DIFFRACTION7chain B and resseq 281:314
8X-RAY DIFFRACTION8chain B and resseq 315:357

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