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- PDB-7eez: crystal structure of maize SHH2 SAWADEE domain -

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Basic information

Entry
Database: PDB / ID: 7eez
Titlecrystal structure of maize SHH2 SAWADEE domain
ComponentsHB transcription factor
KeywordsGENE REGULATION / SAWADEE domain / Maize / SHH2
Function / homology
Function and homology information


chromatin binding / DNA binding / nucleus / metal ion binding
Similarity search - Function
SAWADEE domain / Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2 / SAWADEE domain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
HB transcription factor
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsWang, Y. / Du, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770782 China
CitationJournal: J Integr Plant Biol / Year: 2021
Title: Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2.
Authors: Wang, Y. / Zhou, X. / Luo, J. / Lv, S. / Liu, R. / Du, X. / Jia, B. / Yuan, F. / Zhang, H. / Du, J.
History
DepositionMar 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HB transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1672
Polymers18,1011
Non-polymers651
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.262, 47.262, 137.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

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Components

#1: Protein HB transcription factor / Protein SAWADEE HOMEODOMAIN HOMOLOG 2


Mass: 18101.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100279552, HB131, ZEAMMB73_Zm00001d005584 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7ZYP9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris, pH 6.5, 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 13044 / % possible obs: 99.9 % / Redundancy: 15.5 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.021 / Rrim(I) all: 0.082 / Χ2: 1.75 / Net I/σ(I): 8.8 / Num. measured all: 201808
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.97150.7212750.9740.1850.7441.613100
1.97-2.05150.50612430.9860.130.5231.629100
2.05-2.14150.40512780.9880.1040.4181.658100
2.14-2.25150.2812750.9920.0720.2891.667100
2.25-2.39150.20212660.9960.0520.2091.655100
2.39-2.58150.15812880.9970.0410.1631.814100
2.58-2.84150.11712990.9980.030.1211.976100
2.84-3.25150.07413100.9990.0190.0761.865100
3.25-4.09150.0513360.9990.0130.0521.796100
4.09-5013.80.04514740.9990.0120.0461.81999.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IUR

4iur


Resolution: 1.902→38.953 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 631 4.87 %
Rwork0.2208 12334 -
obs0.2215 12965 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.26 Å2 / Biso mean: 43.0936 Å2 / Biso min: 16.35 Å2
Refinement stepCycle: final / Resolution: 1.902→38.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 1 75 1208
Biso mean--36.85 42.21 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041156
X-RAY DIFFRACTIONf_angle_d0.7751559
X-RAY DIFFRACTIONf_chiral_restr0.03161
X-RAY DIFFRACTIONf_plane_restr0.003209
X-RAY DIFFRACTIONf_dihedral_angle_d13.06438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.902-2.04830.29311550.262348
2.0483-2.25440.28831270.24862413
2.2544-2.58060.21091170.23422433
2.5806-3.2510.27771330.24392462
3.251-38.9530.1977990.19772678
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)
12.9427-2.64782.83187.5511-6.46296.1041-0.0874-0.4435-0.06060.3760.47380.2252-0.9044-0.3033-0.23070.30660.0481-0.00490.3598-0.03790.292323.70622.028650.6157
25.97740.6624-0.5168.4579-0.9841.7929-0.044-0.0180.42630.41280.36810.6631-1.5871-0.2166-0.16140.55220.077-0.00140.2634-0.0280.213322.104425.822251.0419
30.84210.57790.79361.26840.75520.7951-0.10490.09950.37350.01210.0518-0.2878-0.78710.8339-0.05070.7782-0.764-0.33790.6438-0.23170.269837.605832.412247.9103
44.4122-2.7703-4.21782.77271.86334.7759-0.0721-1.5572-0.73360.9390.03240.2695-0.45211.1504-0.15170.8641-0.0721-0.01420.5765-0.02060.42125.543728.291157.9058
55.54572.25651.79375.11990.91287.2808-0.2049-0.15170.13640.13930.1561-0.5-1.07810.92080.00850.2948-0.0961-0.04230.3454-0.03550.266530.108225.046747.2088
62.09352.89780.85574.7766-0.48064.2694-0.2782-0.44160.8624-0.27430.06611.8135-0.3695-1.81350.23490.30110.04710.01970.6663-0.03750.67812.196920.618741.5539
74.97461.60980.57524.66610.96885.48960.1444-0.3511-0.21720.42530.23420.0760.695-1.0903-0.05090.2923-0.13270.02780.421-0.01520.341916.000211.220842.6484
85.51752.73831.36315.59782.00075.9982-0.22160.0041-0.66-0.19670.2686-0.03331.1635-0.512-0.12240.3497-0.06610.01140.2078-0.0010.324919.5589.126242.6943
91.070.62660.10112.20540.71440.67010.11270.0387-0.39140.289-0.23250.63660.1944-1.16380.33890.5168-0.6168-0.00951.3075-0.07080.45062.66446.895835.5406
106.34491.16080.95355.25980.83425.06220.0598-0.2644-0.87220.36030.3204-0.10391.2317-0.5245-0.33590.4221-0.1139-0.03830.35940.00640.372317.82257.154843.0707
114.1367-0.22075.02334.7740.50349.7408-0.50830.7083-0.2515-0.53370.76730.5324-0.6117-1.291-0.29570.2555-0.091-0.0120.61260.02310.271616.499420.395730.7584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 134 through 145 )A134 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 152 )A146 - 152
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 163 )A153 - 163
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 177 )A164 - 177
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 188 )A178 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 194 )A189 - 194
7X-RAY DIFFRACTION7chain 'A' and (resid 195 through 216 )A195 - 216
8X-RAY DIFFRACTION8chain 'A' and (resid 217 through 228 )A217 - 228
9X-RAY DIFFRACTION9chain 'A' and (resid 229 through 239 )A229 - 239
10X-RAY DIFFRACTION10chain 'A' and (resid 240 through 261 )A240 - 261
11X-RAY DIFFRACTION11chain 'A' and (resid 262 through 271 )A262 - 271

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