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- PDB-4bhk: Crystal Structure of Moss Leafy bound to DNA -

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Basic information

Entry
Database: PDB / ID: 4bhk
TitleCrystal Structure of Moss Leafy bound to DNA
Components
  • (MOSS-CR54 DNA) x 2
  • FLORICAULA/LEAFY HOMOLOG 1
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


multicellular organism development / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
Protein LEAFY / Protein LEAFY / Floricaula/leafy protein / Floricaula/Leafy protein, SAM domain / Floricaula/leafy, DNA-binding C-terminal domain / Floricaula/leafy, C-terminal domain superfamily / Floricaula / Leafy protein SAM domain / DNA Binding Domain (C-terminal) Leafy/Floricaula / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Floricaula/leafy-like transcription factor
Similarity search - Component
Biological speciesPHYSCOMITRELLA PATENS (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsNanao, M.H. / Sayou, C. / Dumas, R. / Parcy, F.
CitationJournal: Science / Year: 2014
Title: A Promiscuous Intermediate Underlies the Evolution of Leafy DNA Binding Specificity.
Authors: Sayou, C. / Monniaux, M. / Nanao, M.H. / Moyroud, E. / Brockington, S.F. / Thevenon, E. / Chahtane, H. / Warthmann, N. / Melkonian, M. / Zhang, Y. / Wong, G.K. / Weigel, D. / Parcy, F. / Dumas, R.
History
DepositionApr 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLORICAULA/LEAFY HOMOLOG 1
B: FLORICAULA/LEAFY HOMOLOG 1
W: MOSS-CR54 DNA
X: MOSS-CR54 DNA


Theoretical massNumber of molelcules
Total (without water)57,8804
Polymers57,8804
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-50 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.722, 84.523, 152.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, 0.005134, -0.01133), (0.005875, 0.9978, -0.0664), (0.01097, -0.06646, 0.9977)
Vector: -43.43, -1.373, -52.7)

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Components

#1: Protein FLORICAULA/LEAFY HOMOLOG 1


Mass: 20021.850 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 180-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSCOMITRELLA PATENS (plant) / Plasmid: PPLFY-CTER / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q94IF5
#2: DNA chain MOSS-CR54 DNA


Mass: 8980.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) PHYSCOMITRELLA PATENS (plant)
#3: DNA chain MOSS-CR54 DNA


Mass: 8855.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) PHYSCOMITRELLA PATENS (plant)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.38 Å3/Da / Density % sol: 48.26 % / Description: NONE
Crystal growpH: 5.6
Details: 20 %(V/V) MPD, 0.05 M MES, PH 5.6, 0.1 M MAGNESIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 2010 / Details: KB MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 24528 / % possible obs: 99.1 % / Observed criterion σ(I): -1 / Redundancy: 3.78 % / Biso Wilson estimate: 38.85 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.08
Reflection shellResolution: 2.32→2.46 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.64 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VY2

2vy2


Resolution: 2.32→43.55 Å / Cor.coef. Fo:Fc: 0.9264 / Cor.coef. Fo:Fc free: 0.9065 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1246 5.08 %RANDOM
Rwork0.1962 ---
obs0.1984 24517 --
Displacement parametersBiso mean: 34.66 Å2
Baniso -1Baniso -2Baniso -3
1-4.5881 Å20 Å20 Å2
2---11.1284 Å20 Å2
3---6.5403 Å2
Refine analyzeLuzzati coordinate error obs: 0.296 Å
Refinement stepCycle: LAST / Resolution: 2.32→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2626 1183 0 108 3917
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094051HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.25716HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1683SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes450HARMONIC5
X-RAY DIFFRACTIONt_it4051HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion20.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4233SEMIHARMONIC4
LS refinement shellResolution: 2.32→2.42 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2463 133 4.64 %
Rwork0.2248 2734 -
all0.2258 2867 -
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)
12.561-0.97470.46442.62922.42491.55050.0536-0.11340.0240.1166-0.03570.1921-0.072-0.1833-0.0179-0.009-0.01460.0374-0.0168-0.0024-0.0374-30.4328-4.10325.3155
23.0558-0.16871.08180.7423-0.19220.00110.02510.516-0.1314-0.10760.00030.19340.0894-0.1609-0.0254-0.0662-0.00590.01660.1048-0.0236-0.0203-34.475-9.5213-17.5061
31.6146-0.30030.28881.26380.74632.2440.09830.0840.044-0.144-0.07340.0803-0.1108-0.1491-0.0249-0.0701-0.00250.018-0.02710.0011-0.0727-26.8818-7.1365-8.9441
40.8286-0.2249-0.10561.76371.68643.0369-0.003-0.17210.09730.30030.0344-0.1930.21230.0658-0.0314-0.0122-0.0129-0.0150.0210.0004-0.0316-14.7378-9.81472.1734
54.93930.22180.4232.64060.04311.6410.06670.375-0.0859-0.1818-0.0195-0.21350.01570.2044-0.0472-0.00320.00270.03580.0204-0.003-0.091-12.7291-13.0097-13.4692
64.4491.1214-0.67560.5758-2.12421.3412-0.02490.2057-0.0758-0.1-0.1048-0.17940.03940.32370.12960.01380.01130.0274-0.01780.013-0.051-12.2923-6.5712-57.7863
71.7839-0.27092.26540.6429-0.59342.1129-0.0487-0.3479-0.19250.0636-0.0329-0.14570.0650.16590.0817-0.0669-0.00990.01860.06610.0349-0.0051-9.3137-10.2706-34.188
81.49720.82120.36481.8649-0.5662.6370.0133-0.1111-0.11350.0866-0.0436-0.1224-0.03710.19360.0304-0.05610.02060.0054-0.04750.0025-0.0708-16.2507-8.6431-44.5184
91.21520.3059-0.61162.0247-2.21062.5511-0.03420.13490.1436-0.2181-0.03550.25140.0601-0.02770.06980.0114-0.007-0.0291-0.00860.0069-0.006-28.3638-11.8496-54.2195
106.579-0.4426-0.52262.69870.12631.0480.0479-0.1151-0.12950.1261-0.05670.2242-0.0791-0.23260.0089-0.0234-0.00880.01330.02530.0276-0.0784-30.2854-14.3176-38.6982
112.339-2.91041.84363.29080.05652.5736-0.0093-0.09680.22810.00050.02350.075-0.0987-0.1312-0.01420.0514-0.01460.15080.11660.0337-0.1087-15.705713.4114-68.909
124.39850.2767-2.57733.6736-2.8860.63380.02340.08080.24780.09330.13680.1279-0.1726-0.0898-0.1602-0.0619-0.0150.0311-0.04140.0367-0.147-18.48585.1996-52.8889
131.77682.3275-1.47212.68311.1044.4460.10810.13810.4231-0.41130.1462-0.2853-0.2297-0.1519-0.25430.12110.09110.0918-0.0898-0.0017-0.0794-21.14547.0153-23.182
144.65581.1945-2.77594.19452.68842.53150.0019-0.10830.3069-0.18330.134-0.2189-0.03020.0025-0.1359-0.00010.01150.05810.0064-0.04190.0616-27.035610.31728.3262
150.12370.1823-1.080102.22642.50950.02050.0260.14570.01110.0561-0.12940.03860.1536-0.0766-0.0172-0.04430.10510.0896-0.07020.0651-24.752613.198313.79
161.33442.04690.18920.3276-0.25264.057-0.0230.16480.2743-0.14760.3590.0902-0.42910.0553-0.3360.16260.04340.069-0.13990.0134-0.0967-21.98458.0832-14.1894
170.24672.8624-1.03053.96341.92363.09530.0630.09370.0655-0.0803-0.02260.2081-0.095-0.2214-0.04040.06390.070.049-0.03370.0418-0.105-23.69744.1068-39.7636
186.1614-2.8551-2.83566.25-2.86144.0434-0.02790.0230.07980.27830.15710.1217-0.17520.0035-0.1292-0.0046-0.03040.07110.00640.0699-0.0717-15.30928.0768-61.5946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|189 - 211}
2X-RAY DIFFRACTION2{A|212 - 239}
3X-RAY DIFFRACTION3{A|240 - 284}
4X-RAY DIFFRACTION4{A|285 - 310}
5X-RAY DIFFRACTION5{A|311 - 346}
6X-RAY DIFFRACTION6{B|189 - 211}
7X-RAY DIFFRACTION7{B|212 - 242}
8X-RAY DIFFRACTION8{B|243 - 285}
9X-RAY DIFFRACTION9{B|286 - 310}
10X-RAY DIFFRACTION10{B|311 - 346}
11X-RAY DIFFRACTION11{W|1 - 4}
12X-RAY DIFFRACTION12{W|5 - 10}
13X-RAY DIFFRACTION13{W|11 - 21}
14X-RAY DIFFRACTION14{W|22 - 29}
15X-RAY DIFFRACTION15{X|1 - 6}
16X-RAY DIFFRACTION16{X|7 - 16}
17X-RAY DIFFRACTION17{X|17 - 21}
18X-RAY DIFFRACTION18{X|22 - 29}

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