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- PDB-3jpz: Crystal Structure of Lombricine Kinase -

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Basic information

Entry
Database: PDB / ID: 3jpz
TitleCrystal Structure of Lombricine Kinase
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
NITRATE ION / Lombricine kinase
Similarity search - Component
Biological speciesUrechis caupo (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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 4, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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.language / _software.location / _software.name
Revision 1.5Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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
B: Lombricine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3077
Polymers81,9972
Non-polymers3105
Water15,871881
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lombricine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1233
Polymers40,9991
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Lombricine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1854
Polymers40,9991
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.340, 59.550, 85.850
Angle α, β, γ (deg.)90.000, 105.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lombricine kinase


Mass: 40998.504 Da / Num. of mol.: 2
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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: protein at 30 mg/mL, mixed 1:1 with and equilibrated against 15mM BisTris, 0.2M NaNO3, 1mM DTT, 20% w/v PEG 3350MME, pH 6.8, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 21, 2004 / Details: double focusing mirrors
RadiationMonochromator: Focusing Rh-coated Si mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 69201 / % possible obs: 94.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.131 / Χ2: 2.442 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.793.30.37844960.847192.9
1.79-1.843.40.32144370.924192.6
1.84-1.893.40.35144941.65192.4
1.89-1.943.40.38244193.121191.3
1.94-23.40.21844811.444192.1
2-2.073.30.29644063.231191.5
2.07-2.163.40.18445691.977193.9
2.16-2.263.30.23745773.698194.1
2.26-2.373.40.15646802.44196.3
2.37-2.523.50.14747152.896197.4
2.52-2.723.60.14248113.227198.4
2.72-2.993.70.12147872.625198.5
2.99-3.423.60.1148122.749198.3
3.42-4.313.50.10147262.711196.3
4.31-303.50.09247912.733195.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lombricine kinase ADP complex, 3JQ3

3jq3


Resolution: 1.95→28.487 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.786 / SU ML: 0.36 / Isotropic thermal model: Throughout (+ TLS) / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2560 5.08 %Random
Rwork0.208 ---
obs0.212 50441 95.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.791 Å2 / ksol: 0.449 e/Å3
Displacement parametersBiso max: 140.67 Å2 / Biso mean: 26.288 Å2 / Biso min: 1.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.401 Å20 Å2-0.178 Å2
2---0.443 Å20 Å2
3---0.844 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5719 0 20 881 6620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411610
X-RAY DIFFRACTIONf_angle_d0.71120899
X-RAY DIFFRACTIONf_chiral_restr0.052861
X-RAY DIFFRACTIONf_plane_restr0.0031857
X-RAY DIFFRACTIONf_dihedral_angle_d14.2412946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.9870.3491260.2542511263790
1.987-2.0280.3041440.262540268491
2.028-2.0720.3631470.2692429257688
2.072-2.120.3431380.2472583272193
2.12-2.1730.3181380.2412607274593
2.173-2.2320.281320.2212581271393
2.232-2.2980.2891260.2142646277294
2.298-2.3720.3061410.2132686282796
2.372-2.4570.2751540.2062669282396
2.457-2.5550.2811340.22753288798
2.555-2.6710.2861510.1942704285597
2.671-2.8120.261750.1922735291098
2.812-2.9880.281370.1912758289598
2.988-3.2180.2731440.1912729287399
3.218-3.5420.2751560.1822770292698
3.542-4.0530.2641400.1782685282595
4.053-5.1010.2321260.1712777290397
5.101-28.490.2641510.2262718286994
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)
10.0984-0.2097-0.15310.46410.04060.66450.1307-0.04120.0181-0.1118-0.0201-0.016-0.37940.06540.0780.2108-0.03640.05760.0894-0.02750.054914.44353.827815.8722
20.3369-0.1045-0.76970.09540.14521.4445-0.0851-0.2165-0.01070.07330.04770.03940.12930.4765-0.00250.11820.02830.00990.2292-0.00160.092716.3977-13.823136.1626
30.20570.1021-0.53660.0170.02390.52550.06490.2169-0.0613-0.0269-0.0214-0.0314-0.0179-0.1172-0.00350.16110.0091-0.01040.07380.00260.1198-9.4496-9.444537.1553
40.02920.003-0.0242-0.00520.0093-0.0023-0.02420.10430.01470.15190.18410.18730.1289-0.03060.00060.42890.03690.09910.1180.02810.1784-4.7546-18.997631.0728
5-0.0173-0.05760.00510.138-0.01380.24540.0009-0.0023-0.0124-0.02140.01360.038-0.1373-0.05460.460.2142-0.00720.00630.0667-0.03410.1108-6.4969-5.202742.6912
60.51750.1759-0.44060.2004-0.39931.3881-0.05510.25760.0734-0.0551-0.04-0.01880.2668-0.5858-0.00720.1115-0.04660.01070.33290.00910.0893-33.75069.3707-7.4432
7-0.1621-0.1199-0.13690.3981-0.18161.10270.04110.0712-0.01110.0112-0.00210.0004-0.0611-0.00260.00020.10770.0014-0.00510.1065-0.00190.1219-16.07714.675912.0534
80.2737-0.17350.41670.6278-0.28620.41170.09120.2381-0.18-0.2343-0.09140.23910.22220.0794-0.18630.20470.017-0.04080.0673-0.05460.1088-15.0318-12.165512.6612
90.00570.0089-0.0113-0.03760.0192-0.0079-0.02060.04850.009-0.20950.01820.148-0.1886-0.04830.00040.49920.1199-0.05070.3228-0.09630.4044-6.8137-5.60356.4398
100.4054-0.0726-0.05940.13670.21230.374-0.04020.139-0.17330.0454-0.02110.06150.1782-0.111-0.03810.2228-0.0168-0.00030.08490.00680.174-19.1785-9.603118.622
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 B and resseq 2:93B2 - 93
7X-RAY DIFFRACTION7chain B and resseq 94:279B94 - 279
8X-RAY DIFFRACTION8chain B and resseq 280:307B280 - 307
9X-RAY DIFFRACTION9chain B and resseq 308:318B308 - 318
10X-RAY DIFFRACTION10chain B and resseq 319:364B319 - 364

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