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- PDB-3dxq: Crystal structure of choline/ethanolamine kinase family protein (... -

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Basic information

Entry
Database: PDB / ID: 3dxq
TitleCrystal structure of choline/ethanolamine kinase family protein (NP_106042.1) from MESORHIZOBIUM LOTI at 2.55 A resolution
Componentscholine/ethanolamine kinase family protein
KeywordsTRANSFERASE / NP_106042.1 / choline/ethanolamine kinase family protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Phosphotransferase enzyme family
Function / homology
Function and homology information


Choline/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of choline/ethanolamine kinase family protein (NP_106042.1) from MESORHIZOBIUM LOTI at 2.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / 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

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Assembly

Deposited unit
A: choline/ethanolamine kinase family protein
B: choline/ethanolamine kinase family protein


Theoretical massNumber of molelcules
Total (without water)67,2672
Polymers67,2672
Non-polymers00
Water00
1
A: choline/ethanolamine kinase family protein


Theoretical massNumber of molelcules
Total (without water)33,6341
Polymers33,6341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: choline/ethanolamine kinase family protein


Theoretical massNumber of molelcules
Total (without water)33,6341
Polymers33,6341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.070, 173.620, 39.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
113AA1 - 21 - 2
213BB1 - 21 - 2
321AA3 - 113 - 11
421BB3 - 113 - 11
534AA12 - 1612 - 16
634BB12 - 1612 - 16
744AA19 - 2419 - 24
844BB19 - 2419 - 24
951AA36 - 4236 - 42
1051BB36 - 4236 - 42
1161AA52 - 7452 - 74
1261BB52 - 7452 - 74
1373AA83 - 8783 - 87
1473BB83 - 8783 - 87
1581AA88 - 12588 - 125
1681BB88 - 12588 - 125
1792AA126126
1892BB126126
19101AA127 - 137127 - 137
20101BB127 - 137127 - 137
21111AA149 - 194149 - 194
22111BB149 - 194149 - 194
23122AA195195
24122BB195195
25131AA196 - 258196 - 258
26131BB196 - 258196 - 258
27142AA259259
28142BB259259
29151AA260 - 264260 - 264
30151BB260 - 264260 - 264
31164AA265 - 272265 - 272
32164BB265 - 272265 - 272
33171AA273 - 300273 - 300
34171BB273 - 300273 - 300

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Components

#1: Protein choline/ethanolamine kinase family protein


Mass: 33633.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: NP_106042.1, mll5367 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q98BZ3
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2000M NaNO3, 20.0000% PEG-3350, No Buffer pH 6.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97882,0.97949,0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978821
20.979491
30.918371
ReflectionResolution: 2.55→29.566 Å / Num. obs: 23913 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 61.65 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.55-2.640.6821.48249411193.3
2.64-2.750.5251.99165452697.6
2.75-2.870.3862.58688422398.1
2.87-3.020.2813.59225439798.7
3.02-3.210.1865.29340441798.4
3.21-3.460.118.39557444598.6
3.46-3.80.062139421435998.8
3.8-4.350.04217.79617447298.7
4.35-5.460.03520.39442441099
5.460.02525.99755449598

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.55→29.566 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.893 / SU B: 25.763 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.609 / ESU R Free: 0.328
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1222 5.1 %RANDOM
Rwork0.242 ---
obs0.244 23862 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.477 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å20 Å20 Å2
2---2.99 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 0 0 4456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224573
X-RAY DIFFRACTIONr_bond_other_d0.0020.023123
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9626206
X-RAY DIFFRACTIONr_angle_other_deg0.88937530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8855585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18322.634205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8441543
X-RAY DIFFRACTIONr_chiral_restr0.0770.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02993
X-RAY DIFFRACTIONr_nbd_refined0.2270.21091
X-RAY DIFFRACTIONr_nbd_other0.1910.23131
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22323
X-RAY DIFFRACTIONr_nbtor_other0.0880.22370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.271
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.24
X-RAY DIFFRACTIONr_mcbond_it1.4932985
X-RAY DIFFRACTIONr_mcbond_other0.32531189
X-RAY DIFFRACTIONr_mcangle_it2.37854612
X-RAY DIFFRACTIONr_scbond_it4.16381814
X-RAY DIFFRACTIONr_scangle_it5.501111592
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
3008TIGHT POSITIONAL0.040.05
262MEDIUM POSITIONAL0.40.25
50LOOSE POSITIONAL0.365
3008TIGHT THERMAL0.321
262MEDIUM THERMAL0.933
50LOOSE THERMAL4.5110
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 96 -
Rwork0.343 1567 -
all-1663 -
obs--96.63 %
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)
11.34380.59680.14252.33770.78040.91470.047-0.07770.21440.1359-0.15060.4617-0.1895-0.28290.1036-0.08540.02-0.07940.0069-0.01110.017721.6167104.21442.0293
21.62540.0925-0.00291.07060.38350.14110.0284-0.0347-0.04870.0084-0.11680.02130.1974-0.09850.0884-0.0103-0.0708-0.0651-0.07860.0332-0.134230.781863.974738.0449
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3002 - 301
2X-RAY DIFFRACTION2BB1 - 3002 - 301

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