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- PDB-3lm2: Crystal structure of Putative kinase. (17743352) from AGROBACTERI... -

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Basic information

Entry
Database: PDB / ID: 3lm2
TitleCrystal structure of Putative kinase. (17743352) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.70 A resolution
ComponentsPutative kinase
KeywordsTRANSFERASE / Putative kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative kinase. (17743352) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative kinase
B: Putative kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4084
Polymers50,2842
Non-polymers1242
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-11 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.907, 49.598, 57.328
Angle α, β, γ (deg.)97.980, 104.640, 109.970
Int Tables number1
Space group name H-MP1
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative kinase


Mass: 25141.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: 17743352, AGR_L_95, Atu4836 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9CH74
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.39 Å3/Da / Density % sol: 48.46 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 20.0000% polyethylene glycol 3350, 0.2000M calcium acetate, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.96109,0.97949,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 7, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961091
20.979491
30.979361
ReflectionResolution: 1.7→29.13 Å / Num. obs: 48619 / % possible obs: 85.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.125 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.1512.189687931177.9
1.76-1.830.1142.895968477183.4
1.83-1.910.0963.695308461184
1.91-2.020.0844.6105639466184.9
2.02-2.140.075.692588354185.8
2.14-2.310.0676.4100509141186.2
2.31-2.540.0617.697048914187.6
2.54-2.90.0568.596728961188.7
2.9-3.660.0549.599389371189.7
3.66-29.130.0511094949136188.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.13 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 4.947 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.095
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. 4. THE TLS GROUP DEFINITIONS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. 5. ETHYLNE GLYCOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2471 5.1 %RANDOM
Rwork0.16 ---
obs0.161 48619 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 71.7 Å2 / Biso mean: 18.481 Å2 / Biso min: 3.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å22 Å20.41 Å2
2--3.65 Å21.28 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 8 380 3746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223622
X-RAY DIFFRACTIONr_bond_other_d0.0010.022461
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9674941
X-RAY DIFFRACTIONr_angle_other_deg0.93836035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62824.424165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48415618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3991525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
X-RAY DIFFRACTIONr_mcbond_it0.8271.52286
X-RAY DIFFRACTIONr_mcbond_other0.2391.5955
X-RAY DIFFRACTIONr_mcangle_it1.4323669
X-RAY DIFFRACTIONr_scbond_it2.24331336
X-RAY DIFFRACTIONr_scangle_it3.5914.51243
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 173 -
Rwork0.224 3139 -
all-3312 -
obs--87.34 %
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)
119.618210.9473.556738.10511.592822.7813-0.15890.0436-2.4265-1.0065-0.4695-0.25342.73110.0840.62840.72360.09170.00070.15510.0350.631811.13813.08659.363
24.56911.5039-1.6215.0665-1.57251.75390.2874-0.80660.27520.4435-0.16650.1205-0.41740.1582-0.12090.2305-0.0503-0.00380.178-0.06810.111910.70932.83661.515
32.64190.7127-0.3361.3163-0.47321.69120.0667-0.210.06130.0549-0.0777-0.1429-0.14140.13610.0110.1521-0.0057-0.01030.0403-0.0060.156915.4532.13651.421
46.34830.32921.22233.1491-1.47315.0693-0.0350.02470.4219-0.0774-0.03020.0626-0.41710.12120.06520.1577-0.02850.00110.0510.01680.186216.68837.04745.374
54.05580.83490.32230.9207-0.25391.39980.0766-0.3508-0.1156-0.0108-0.08010.03060.052-0.01350.00350.1615-0.0097-0.00940.0352-0.01410.14382.22326.42349.965
65.2047-1.712-0.39765.4085-0.49542.02560.03630.02421.24970.28560.0402-0.3474-0.4695-0.095-0.07650.25030.0226-0.01270.0096-0.01820.4129-6.41543.44642.913
73.0039-0.7042-0.09142.8994-0.74053.2462-0.0192-0.09440.3410.10080.07650.1199-0.4731-0.551-0.05730.19720.06710.00330.1056-0.03450.2239-13.74836.65546.371
845.3197-3.517333.67990.2836-2.933635.8817-2.4669-1.02271.81290.22060.1651-0.1827-1.7841-0.44482.30181.37230.3460.08280.3884-0.30041.0486-7.31641.28957.307
99.717-1.97512.24181.426-1.16651.0752-0.1218-0.8520.22410.19760.07510.0343-0.0657-0.20020.04670.232-0.02280.01210.2553-0.07220.1872-6.13229.51557.233
1010.7388-0.24715.52813.19491.06723.29490.5638-0.3387-0.983-0.069-0.02310.01790.2957-0.184-0.54070.4531-0.0826-0.17340.06540.07640.39864.44316.40752.688
1115.47483.44321.099920.62340.7641.9240.14560.5102-1.66690.8069-0.0204-0.10830.6676-0.3051-0.12530.3257-0.0810.00350.1439-0.12440.3172-8.7527.6525.521
122.6501-0.8341-0.01186.7956-0.81813.55370.09640.7351-0.0202-0.6007-0.1844-0.18510.23630.08780.0880.19410.00680.00840.3062-0.04820.0907-7.17518.09415.885
132.00490.10040.25191.43720.12061.06190.02090.42610.0257-0.0781-0.02470.06410.0722-0.16330.00370.1411-0.0003-0.01010.1676-0.01640.1273-12.322.80724.491
142.97330.02530.07040.4905-0.11641.0362-0.00970.3211-0.0726-0.00190.00780.00440.0411-0.06250.00190.1501-0.005-0.00780.0779-0.01220.1287-1.85422.82129.655
1510.83622.986-2.44486.548-2.07375.37120.16950.19440.98110.0256-0.01440.0646-0.54580.4048-0.15510.2533-0.04030.04210.0780.0690.22659.47939.85130.496
167.69330.4513-4.52584.5436-1.27859.82960.29540.93570.9495-0.06620.15010.1509-0.6124-0.9803-0.44560.14390.02910.0120.36390.20980.199610.01439.11116.859
172.1122-1.28230.00974.0588-7.42116.80290.15720.15380.24380.1215-0.1689-0.1504-0.4570.23920.01170.1744-0.03110.00940.1760.04780.180117.39933.42525.184
184.4654-1.53222.03245.4154-3.75715.87450.03280.80170.0513-0.5879-0.1466-0.1890.14390.33410.11380.18340.00640.03590.2614-0.0030.135513.93824.84421.104
1911.73165.2497-0.23082.8416-0.59840.5058-0.22760.9531-0.497-0.19690.2632-0.17580.12430.1442-0.03560.19340.00920.02230.2349-0.10910.17498.82717.54722.666
2018.884310.25139.06125.58684.60988.85870.4357-0.1879-0.98080.2046-0.1055-0.54070.44990.0116-0.33020.313-0.0161-0.03780.05670.00310.281-0.7579.78433.596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 6
2X-RAY DIFFRACTION2A7 - 31
3X-RAY DIFFRACTION3A32 - 73
4X-RAY DIFFRACTION4A74 - 85
5X-RAY DIFFRACTION5A86 - 131
6X-RAY DIFFRACTION6A132 - 163
7X-RAY DIFFRACTION7A164 - 188
8X-RAY DIFFRACTION8A189 - 196
9X-RAY DIFFRACTION9A197 - 217
10X-RAY DIFFRACTION10A218 - 225
11X-RAY DIFFRACTION11B4 - 9
12X-RAY DIFFRACTION12B10 - 31
13X-RAY DIFFRACTION13B32 - 71
14X-RAY DIFFRACTION14B72 - 135
15X-RAY DIFFRACTION15B136 - 149
16X-RAY DIFFRACTION16B150 - 163
17X-RAY DIFFRACTION17B164 - 180
18X-RAY DIFFRACTION18B181 - 197
19X-RAY DIFFRACTION19B198 - 217
20X-RAY DIFFRACTION20B218 - 225

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