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- PDB-3jq3: Crystal Structure of Lombricine Kinase, complexed with substrate ADP -

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Basic information

Entry
Database: PDB / ID: 3jq3
TitleCrystal Structure of Lombricine Kinase, complexed with substrate ADP
ComponentsLombricine kinase
KeywordsTRANSFERASE / Mixed alpha / beta / Kinase
Function / homology
Function and homology information


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
ADENOSINE-5'-DIPHOSPHATE / Lombricine kinase
Similarity search - Component
Biological speciesUrechis caupo (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsBush, D.J. / Kirillova, O. / Clark, S.A. / Fabiola, F. / Somasundaram, T. / Chapman, M.S.
Citation
Journal: J.Biol.Chem. / Year: 2011
Title: The structure of lombricine kinase: implications for phosphagen kinase conformational changes.
Authors: Bush, D.J. / Kirillova, O. / Clark, S.A. / Davulcu, O. / Fabiola, F. / Xie, Q. / Somasundaram, T. / Ellington, W.R. / Chapman, M.S.
#1: Journal: BIOCHEM.BIOPHYS.RES.COMMUN. / Year: 2002
Title: Cloning and expression of a lombricine kinase from an echiuroid worm: insights into structural correlates of substrate specificity
Authors: Ellington, W.R. / Bush, J.
History
DepositionSep 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.5Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Lombricine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4262
Polymers40,9991
Non-polymers4271
Water3,027168
1
A: Lombricine kinase
hetero molecules

A: Lombricine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8514
Polymers81,9972
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.692, 77.986, 141.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

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Components

#1: Protein Lombricine kinase /


Mass: 40998.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Urechis caupo (invertebrata) / Plasmid: pETblue-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3)pLacI / References: UniProt: Q8T6T7, EC: 2.7.3.5
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: protein at 30 mg/mL in 50mM taurocyamine, 40mM ADP & 5mM MgCl2, mixed 1:1 with and equilibrated against 15mM BisTris, 0.2M NaNO3, 1mM DTT, 20% w/v PEG 3350MME, pH 5.8, VAPOR DIFFUSION, ...Details: protein at 30 mg/mL in 50mM taurocyamine, 40mM ADP & 5mM MgCl2, mixed 1:1 with and equilibrated against 15mM BisTris, 0.2M NaNO3, 1mM DTT, 20% w/v PEG 3350MME, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.99997 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2005 / Details: double focusing mirrors
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 13213 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.122 / Χ2: 1.344 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 5.23 / Num. unique all: 1302 / Χ2: 0.456 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CNSphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model built from creatine kinase, 1qk1

1qk1


Resolution: 2.503→19.994 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.34 / Isotropic thermal model: Throughout + TLS / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 482 3.66 %Random
Rwork0.178 ---
obs0.181 13186 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.974 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 84.73 Å2 / Biso mean: 27.429 Å2 / Biso min: 3.28 Å2
Baniso -1Baniso -2Baniso -3
1-2.363 Å20 Å20 Å2
2---1.193 Å20 Å2
3----1.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.503→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 27 168 3061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.03
X-RAY DIFFRACTIONf_angle_deg0.69
X-RAY DIFFRACTIONf_dihedral_angle_d15.4
LS refinement shellResolution: 2.5→2.86 Å
RfactorNum. reflection% reflection
Rfree0.329 151 -
Rwork0.218 --
obs-4316 99 %
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)
11.79730.9783-0.99850.58160.142.23850.00420.27360.1506-0.16360.0581-0.0094-0.2091-0.318100.1711-0.0220.02310.1466-0.00230.1214-4.8717-2.539419.7806
20.73830.7145-0.62120.9102-0.7911.7347-0.0269-0.0418-0.0389-0.00640.0145-0.10880.00290.132600.06380.00330.01660.1009-0.03090.136220.37997.489121.7857
30.1079-0.06360.09340.00840.00450.3935-0.12130.06710.1265-0.07730.14260.42260.0087-0.58870.00230.2197-0.0439-0.05860.21760.05930.25329.628125.08914.3729
40.1362-0.0674-0.0067-0.0140.00770.0811-0.2395-0.2554-0.98280.2538-0.07190.76030.2852-0.1616-0.00180.53090.0440.02290.33570.09480.617110.154926.352316.7007
50.3644-0.0805-0.29951.0399-0.20410.1241-0.14340.09730.1191-0.3210.23310.4762-0.0355-0.16890.00290.2684-0.1138-0.03080.19230.03270.13913.989820.29140.2178
6-0.1798-0.1186-0.0306-0.09840.06380.0216-0.0784-0.2145-0.01830.254-0.30770.25060.015-0.218-0.00480.805-0.10970.06890.2925-0.0210.767615.105318.739317.7012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 3:93A3 - 93
2X-RAY DIFFRACTION2chain A and resseq 94:279A94 - 279
3X-RAY DIFFRACTION3chain A and resseq 280:307A280 - 307
4X-RAY DIFFRACTION4chain A and resseq 308:318A308 - 318
5X-RAY DIFFRACTION5chain A and resseq 319:366A319 - 366
6X-RAY DIFFRACTION6chain A and resseq 400:400A400

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