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- PDB-1wn0: Crystal Structure of Histidine-containing Phosphotransfer Protein... -

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Basic information

Entry
Database: PDB / ID: 1wn0
TitleCrystal Structure of Histidine-containing Phosphotransfer Protein, ZmHP2, from maize
Componentshistidine-containing phosphotransfer protein
KeywordsSIGNALING PROTEIN / four-helix bundle / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of cytokinin-activated signaling pathway / protein histidine kinase binding / cytokinin-activated signaling pathway / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorylation / nucleus / cytosol / cytoplasm
Similarity search - Function
HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histidine-containing phosphotransfer protein
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSugawara, H. / Kawano, Y. / Hatakeyama, T. / Yamaya, T. / Kamiya, N. / Sakakibara, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structure of the histidine-containing phosphotransfer protein ZmHP2 from maize
Authors: Sugawara, H. / Kawano, Y. / Hatakeyama, T. / Yamaya, T. / Kamiya, N. / Sakakibara, H.
History
DepositionJul 24, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: histidine-containing phosphotransfer protein
B: histidine-containing phosphotransfer protein
C: histidine-containing phosphotransfer protein
D: histidine-containing phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)64,9024
Polymers64,9024
Non-polymers00
Water1,856103
1
A: histidine-containing phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)16,2251
Polymers16,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: histidine-containing phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)16,2251
Polymers16,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: histidine-containing phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)16,2251
Polymers16,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: histidine-containing phosphotransfer protein


Theoretical massNumber of molelcules
Total (without water)16,2251
Polymers16,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.800, 81.410, 89.500
Angle α, β, γ (deg.)90.00, 123.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
histidine-containing phosphotransfer protein


Mass: 16225.483 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: Zmhp2 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9SLX1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 50mM ammonium sulfate, 100mM sodium acetate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL45XU11
SYNCHROTRONSPring-8 BL45XU20.9791, 0.9793, 0.982
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 28, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamond trichromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.97931
40.9821
ReflectionResolution: 2.2→20 Å / Num. obs: 42707 / % possible obs: 94.1 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD
Starting model: selenomethionine labeled protein

Resolution: 2.2→19.84 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.951 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2141 5 %RANDOM
Rwork0.209 ---
all0.211 42707 --
obs0.211 40566 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4175 0 0 103 4278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0224226
X-RAY DIFFRACTIONr_bond_other_d0.0020.023832
X-RAY DIFFRACTIONr_angle_refined_deg2.5561.9575687
X-RAY DIFFRACTIONr_angle_other_deg1.17838932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775526
X-RAY DIFFRACTIONr_chiral_restr0.1890.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024740
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02826
X-RAY DIFFRACTIONr_nbd_refined0.2480.21064
X-RAY DIFFRACTIONr_nbd_other0.2530.24076
X-RAY DIFFRACTIONr_nbtor_other0.1020.22428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3160.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.212
X-RAY DIFFRACTIONr_mcbond_it1.5421.52632
X-RAY DIFFRACTIONr_mcangle_it2.71324211
X-RAY DIFFRACTIONr_scbond_it4.5931594
X-RAY DIFFRACTIONr_scangle_it7.424.51476
LS refinement shellHighest resolution: 2.2 Å / Num. reflection Rwork: 2847 / Total num. of bins used: 20
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)
10.7444-0.0421-0.4104-0.0002-0.12690.48360.03120.01440.01310.00570.02810.0041-0.0501-0.0328-0.05930.04310.00460.00160.07870.01710.051189.018919.736114.129
20.2469-0.0367-0.18750.2695-0.07081.4006-0.0279-0.0501-0.03730.01380.0007-0.0493-0.00280.03750.02710.00120.0090.00260.0782-0.0020.060857.7854-18.4723-12.0213
30.22890.0680.0340.43310.0757-0.0202-0.04490.00460.01490.02730.0473-0.0270.0199-0.0047-0.00240.0327-0.0015-0.00820.085-0.00650.043248.78690.48624.4026
40.111-0.00030.00090.56350.28550.19780.0283-0.003-0.0102-0.040.00280.0579-0.0158-0.002-0.03120.01690.001-0.00890.075900.058978.26990.503128.5457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 1399 - 139
2X-RAY DIFFRACTION2BB11 - 13811 - 138
3X-RAY DIFFRACTION3CC5 - 1425 - 142
4X-RAY DIFFRACTION4DD5 - 1425 - 142

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