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- PDB-4ix5: Crystal structure of a Stt7 homolog from Micromonas algae in comp... -

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Basic information

Entry
Database: PDB / ID: 4ix5
TitleCrystal structure of a Stt7 homolog from Micromonas algae in complex with AMP-PNP
ComponentsMsStt7d protein
KeywordsTRANSFERASE / protein kinase / canonical protein kinase fold / ATP binding
Function / homology
Function and homology information


protein kinase activity / ATP binding / metal ion binding
Similarity search - Function
PDZ superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...PDZ superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein kinase domain-containing protein
Similarity search - Component
Biological speciesMicromonas (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 1.7 Å
AuthorsGuo, J. / Wei, X. / Li, M. / Pan, X. / Chang, W. / Liu, Z.
CitationJournal: Protein Cell / Year: 2013
Title: Structure of the catalytic domain of a state transition kinase homolog from Micromonas algae
Authors: Guo, J. / Wei, X. / Li, M. / Pan, X. / Chang, W. / Liu, Z.
History
DepositionJan 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: MsStt7d protein
B: MsStt7d protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5517
Polymers75,4662
Non-polymers1,0855
Water11,259625
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.860, 132.610, 55.180
Angle α, β, γ (deg.)90.00, 116.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MsStt7d protein


Mass: 37732.906 Da / Num. of mol.: 2 / Fragment: UNP residues 151-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonas (plant) / Strain: RCC299 / Gene: STT7 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C1EBN1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, 200mM MgCl2, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97854 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.7→33.15 Å / Num. all: 76423 / Num. obs: 75812 / % possible obs: 99.2 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.1 / Num. unique all: 11076 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: Difference Fourier / Resolution: 1.7→28.628 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 3735 5.04 %RANDOM
Rwork0.1725 ---
all0.1779 75801 --
obs0.1739 74080 97.73 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.726 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 26.5682 Å2
Baniso -1Baniso -2Baniso -3
1-1.2773 Å20 Å2-5.4573 Å2
2---3.0134 Å2-0 Å2
3---1.7361 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 65 625 5936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065463
X-RAY DIFFRACTIONf_angle_d0.9997318
X-RAY DIFFRACTIONf_chiral_restr0.067792
X-RAY DIFFRACTIONf_plane_restr0.004974
X-RAY DIFFRACTIONf_dihedral_angle_d12.6731984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.76080.27443360.2076703703993
1.7608-1.83120.2353630.19396787715095
1.8312-1.91460.2323700.18386901727196
1.9146-2.01550.22663650.17847034739998
2.0155-2.14170.20433780.1687084746299
2.1417-2.3070.20523460.17077134748099
2.307-2.53910.2114290.17247067749699
2.5391-2.90620.22773720.18717180755299
2.9062-3.66020.19033970.17671987595100
3.6602-28.63160.16313790.153172577636100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.001-0.0004-0.00310.00050.00340.0224-0.0109-0.0047-0.0015-0.0221-0.00140.0005-0.0305-0.02760.00930.44330.09210.01650.12910.00760.096164.378516.966235.0914
20.02990.0156-0.00650.0283-0.00780.00320.0161-0.0475-0.0009-0.0196-0.0382-0.00760.05790.03370.02460.16130.0683-0.04670.17070.00480.0651.812535.983233.2665
30.2990.09160.03830.0766-0.03290.0441-0.0290.0373-0.04870.0343-0.0059-0.01150.0020.02030.03110.1527-0.1022-0.01390.23110.04480.139136.085636.055430.1739
40.14710.00340.00910.4026-0.22460.12530.07330.0343-0.044-0.11530.09580.02460.0301-0.0855-0.09050.0267-0.01810.05440.13510.0020.019736.967640.075425.3655
50.19160.01080.17850.00050.01090.16680.0935-0.0001-0.106-0.03220.02750.03290.0717-0.0023-0.10470.1417-0.0246-0.01480.04210.00110.08743.277132.033718.0906
60.00450.0057-0.02350.10520.05410.1988-0.0234-0.0061-0.08690.0012-0.0015-0.0738-0.00770.05730.01950.0399-0.0074-0.00830.04350.00850.104551.504135.248416.8238
70.00910.03240.04610.16710.23530.33-0.0013-0.0992-0.05910.1237-0.0166-0.03220.0895-0.0317-0.0231-0.00570.0146-0.09770.03510.121-0.348.337346.380624.9412
80.0624-0.00160.01650.0126-0.00320.00930.00830.0015-0.0040.01290.0085-0.0050.0074-0.0099-0.0090.6855-0.0846-0.08520.67930.09040.718938.980625.498530.3566
90.0007-0.00180.00260.0065-0.00630.0043-0.0129-0.0083-0.01770.02820.01320.01830.0544-0.0140.00130.18830.00380.05460.05980.06010.048341.45330.772228.1806
100.0030.0088-0.00220.0396-0.0009-0.0007-0.03410.0860.0353-0.0023-0.01770.02940.0427-0.06180.0162-0.0607-0.05370.1140.05520.0896-0.102836.817646.106923.4111
110.012-0.02560.04010.082-0.0940.1758-0.0212-0.05380.10480.00430.06190.0608-0.0055-0.1542-0.02660.04120.00830.01490.13730.0040.137626.445656.560410.9661
120.38320.1306-0.1220.1750.04110.28010.0301-0.040.0708-0.0198-0.00060.047-0.11780.0116-0.00920.0177-0.0058-0.01060.0050.00190.021140.996161.338311.5096
130.04610.03740.03580.03790.03080.04040.0022-0.1048-0.04250.0184-0.0661-0.0018-0.01910.00940.06170.0258-0.01740.01120.09660.00050.047640.427251.840414.878
140.08590.0267-0.02690.0085-0.00810.0052-0.0113-0.040.0123-0.0165-0.0158-0.08840.03270.24390.0154-0.22890.00250.09770.10260.00180.030757.292646.250911.3178
150.05620.046-0.09720.0348-0.08560.17-0.0603-0.0519-0.0444-0.0908-0.018-0.07320.12520.19450.0722-0.13290.05940.12780.1362-0.0439-0.03354.805346.89882.1542
160.0150.00660.00140.0115-0.02350.0620.01520.00670.0199-0.0112-0.0146-0.0354-0.010.0108-0.0043-0.0571-0.06080.08420.14660.1110.006760.704655.46634.0062
170.15710.18130.17080.64420.43160.3207-0.11790.1520.0314-0.31480.0350.0695-0.15250.04640.06740.0655-0.0357-0.0374-0.02070.175-0.313337.698254.9152-4.0522
180.40690.30730.15520.4758-0.0610.2668-0.12050.13010.1362-0.22360.02520.0954-0.03250.06080.06940.0929-0.0215-0.04360.07170.04080.075434.654662.0075-6.0436
190.33640.3458-0.01110.3577-0.01530.5298-0.0363-0.02150.1030.0151-0.06970.0533-0.11850.11020.07090.0648-0.02090.00240.07580.0330.065645.708365.15173.2762
200.027-0.00440.00210.0181-0.00840.0039-0.0179-0.0129-0.00460.00050.0045-0.0025-0.0084-0.00610.010.4130.11020.0390.42390.07170.323928.653982.406311.5351
210.1150.00810.08480.19130.04570.06760.05160.0644-0.04210.11180.0161-0.00130.09410.0103-0.08050.1474-0.0293-0.06360.07980.03140.092426.119938.956-16.4703
220.0021-0.00490.00030.01470.0050.008-0.0096-0.0035-0.0277-0.01550.01940.0349-0.0039-0.0106-0.00950.13990.0113-0.0760.17080.070.250116.366528.925-2.6382
230.01510.0349-0.00520.11280.02940.05540.0316-0.01150.0167-0.00190.0026-0.0015-0.03550.0259-0.02490.31760.00670.03530.2034-0.06130.207226.182129.923510.2236
240.0567-0.0083-0.03390.12330.1120.24310.0046-0.0319-0.02970.02630.12290.10340.0014-0.04-0.1202-0.0161-0.0455-0.02340.04060.06290.130724.710725.15344.2229
250.13740.11840.06410.32720.02460.1670.0549-0.00890.0225-0.04760.0265-0.1112-0.0401-0.0005-0.07250.016-0.02020.03750.0273-0.00270.093236.039834.77932.2056
260.2435-0.19950.0160.2783-0.17330.22510.08950.03910.0469-0.134-0.033-0.0199-0.0194-0.0115-0.04530.13520.03660.02660.05560.01310.073938.233529.0051-5.2572
270.01410.01070.00080.4495-0.44720.43590.01540.0541-0.048-0.2540.0570.15370.1879-0.119-0.07980.08140.0156-0.0326-0.01390.01990.039127.492725.8889-2.3355
280.0805-0.00060.02870.0616-0.02380.02-0.0267-0.02340.01070.06630.0778-0.0288-0.0179-0.0014-0.03230.10450.0676-0.01030.1265-0.04610.072132.693915.109217.8256
290.04030.01270.0740.3915-0.24680.3174-0.0302-0.0417-0.0153-0.04160.0819-0.00860.0489-0.0892-0.0340.07290.00720.02270.08340.02220.060933.79973.203418.7747
300.14630.04370.09150.03660.040.06320.10950.0295-0.0092-0.1875-0.0582-0.07620.1344-0.0047-0.06050.16750.03450.0595-0.05110.03910.049841.09346.54252.4276
310.17720.13520.06230.2372-0.09470.18020.00470.00320.1207-0.0687-0.0868-0.0944-0.0044-0.02610.06680.0353-0.0011-0.00040.01970.00520.104738.319615.8697.6662
320.2089-0.12980.150.2291-0.05030.12220.01490.0330.1528-0.0983-0.1257-0.05290.0551-0.03420.05730.0786-0.0117-0.0111-0.0090.00390.074535.821914.61312.5585
330.0420.0131-0.020.0066-0.00780.0097-0.01550.0008-0.00210.0281-0.0842-0.06990.00770.05640.07220.28680.00540.08150.20890.13010.299548.31621.4772-9.6148
340.01350.02640.02380.1122-0.04090.1464-0.09080.03610.07680.0069-0.0949-0.1056-0.05190.07640.15670.0484-0.0329-0.10310.05890.10660.437752.815121.34237.4576
350.1061-0.14860.09290.4967-0.17270.2804-0.02270.08090.3819-0.0329-0.2148-0.53330.07680.14930.21120.03890.05590.09620.06790.20890.290452.553114.5480.8484
360.04670.0440.00620.0565-0.08390.4561-0.0974-0.02710.03730.1557-0.17-0.1753-0.2110.09030.22780.1388-0.0088-0.1690.08070.03340.28854.510211.477921.1262
370.00250.0050.0050.02410.01350.0108-0.01770.00770.0347-0.0016-0.02510.0068-0.00980.02350.03190.42830.063-0.23970.4639-0.03220.542557.23178.248928.5411
380.1705-0.2549-0.05790.41820.01420.3274-0.02410.01980.14890.0555-0.1446-0.28080.08770.13170.14590.10720.03980.0050.11010.06330.171551.15492.764818.0722
390.1382-0.06250.01750.07590.06970.1195-0.05650.03020.05820.0614-0.0519-0.06970.18020.07090.06870.17270.11820.0896-0.02870.07460.177850.3341.84056.0091
400.04090.0375-0.00480.0368-0.00120.0201-0.03780.01520.06160.0213-0.042-0.1035-0.035-0.00580.06150.31220.0583-0.18030.1394-0.00510.358532.251-16.074114.3677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 151:157)A151 - 157
2X-RAY DIFFRACTION2(CHAIN A AND RESID 158:166)A158 - 166
3X-RAY DIFFRACTION3(CHAIN A AND RESID 167:179)A167 - 179
4X-RAY DIFFRACTION4(CHAIN A AND RESID 180:198)A180 - 198
5X-RAY DIFFRACTION5(CHAIN A AND RESID 199:206)A199 - 206
6X-RAY DIFFRACTION6(CHAIN A AND RESID 207:216)A207 - 216
7X-RAY DIFFRACTION7(CHAIN A AND RESID 217:242)A217 - 242
8X-RAY DIFFRACTION8(CHAIN A AND RESID 243:249)A243 - 249
9X-RAY DIFFRACTION9(CHAIN A AND RESID 250:258)A250 - 258
10X-RAY DIFFRACTION10(CHAIN A AND RESID 259:267)A259 - 267
11X-RAY DIFFRACTION11(CHAIN A AND RESID 268:291)A268 - 291
12X-RAY DIFFRACTION12(CHAIN A AND RESID 292:311)A292 - 311
13X-RAY DIFFRACTION13(CHAIN A AND RESID 312:338)A312 - 338
14X-RAY DIFFRACTION14(CHAIN A AND RESID 339:359)A339 - 359
15X-RAY DIFFRACTION15(CHAIN A AND RESID 360:386)A360 - 386
16X-RAY DIFFRACTION16(CHAIN A AND RESID 387:395)A387 - 395
17X-RAY DIFFRACTION17(CHAIN A AND RESID 396:440)A396 - 440
18X-RAY DIFFRACTION18(CHAIN A AND RESID 441:471)A441 - 471
19X-RAY DIFFRACTION19(CHAIN A AND RESID 472:491)A472 - 491
20X-RAY DIFFRACTION20(CHAIN A AND RESID 492:496)A492 - 496
21X-RAY DIFFRACTION21(CHAIN B AND RESID 151:166)B151 - 166
22X-RAY DIFFRACTION22(CHAIN B AND RESID 167:172)B167 - 172
23X-RAY DIFFRACTION23(CHAIN B AND RESID 173:180)B173 - 180
24X-RAY DIFFRACTION24(CHAIN B AND RESID 181:198)B181 - 198
25X-RAY DIFFRACTION25(CHAIN B AND RESID 199:208)B199 - 208
26X-RAY DIFFRACTION26(CHAIN B AND RESID 209:218)B209 - 218
27X-RAY DIFFRACTION27(CHAIN B AND RESID 219:265)B219 - 265
28X-RAY DIFFRACTION28(CHAIN B AND RESID 266:275)B266 - 275
29X-RAY DIFFRACTION29(CHAIN B AND RESID 276:295)B276 - 295
30X-RAY DIFFRACTION30(CHAIN B AND RESID 296:314)B296 - 314
31X-RAY DIFFRACTION31(CHAIN B AND RESID 315:328)B315 - 328
32X-RAY DIFFRACTION32(CHAIN B AND RESID 329:345)B329 - 345
33X-RAY DIFFRACTION33(CHAIN B AND RESID 346:356)B346 - 356
34X-RAY DIFFRACTION34(CHAIN B AND RESID 357:374)B357 - 374
35X-RAY DIFFRACTION35(CHAIN B AND RESID 375:413)B375 - 413
36X-RAY DIFFRACTION36(CHAIN B AND RESID 414:440)B414 - 440
37X-RAY DIFFRACTION37(CHAIN B AND RESID 441:446)B441 - 446
38X-RAY DIFFRACTION38(CHAIN B AND RESID 447:471)B447 - 471
39X-RAY DIFFRACTION39(CHAIN B AND RESID 472:491)B472 - 491
40X-RAY DIFFRACTION40(CHAIN B AND RESID 492:500)B492 - 500

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