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- PDB-1ut4: Structure of the conserved domain of ANAC, a member of the NAC fa... -

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Basic information

Entry
Database: PDB / ID: 1ut4
TitleStructure of the conserved domain of ANAC, a member of the NAC family of transcription factors
ComponentsNO APICAL MERISTEM PROTEIN
KeywordsTRANSCRIPTION REGULATION / TRANSCRIPTION / TRANSCRIPTION FACTOR / DNA BINDING / ABSCISIC ACID RESPONSE / ARABIDOPSIS THALIANA / NAC DOMAIN
Function / homology
Function and homology information


response to water deprivation / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
NAC domain / NAC domain / NAC domain superfamily / No apical meristem (NAM) protein / NAC domain profile. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
NAC domain-containing protein 19
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsErnst, H.A. / Olsen, A.N. / Skriver, K. / Larsen, S. / Lo Leggio, L.
Citation
Journal: Embo Rep. / Year: 2004
Title: Structure of the Conserved Domain of Anac, a Member of the Nac Family of Transcription Factors
Authors: Ernst, H.A. / Olsen, A.N. / Skriver, K. / Larsen, S. / Lo Leggio, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Preliminary Crystallographic Analysis of the Nac Domain of Anac, a Member of the Plant-Specific Nac Transcription Factor Family
Authors: Olsen, A. / Ernst, H. / Lo Leggio, L. / Johansson, E. / Larsen, S. / Skriver, K.
History
DepositionDec 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NO APICAL MERISTEM PROTEIN
B: NO APICAL MERISTEM PROTEIN


Theoretical massNumber of molelcules
Total (without water)39,5612
Polymers39,5612
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.953, 75.224, 80.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHE4AA16 - 2019 - 23
21PROPROPHEPHE4BB16 - 2019 - 23
12TYRTYRASPASP1AA21 - 2424 - 27
22TYRTYRASPASP1BB21 - 2424 - 27
13GLUGLUGLUGLU3AA2528
23GLUGLUGLUGLU3BB2528
14GLUGLULEULEU1AA26 - 3229 - 35
24GLUGLULEULEU1BB26 - 3229 - 35
15ARGARGLYSLYS6AA34 - 3537 - 38
25ARGARGLYSLYS6BB34 - 3537 - 38
16ILEILEILEILE3AA4952
26ILEILEILEILE3BB4952
17ASPASPASPASP1AA5053
27ASPASPASPASP1BB5053
18LEULEULEULEU2AA5154
28LEULEULEULEU2BB5154
19TYRTYRTYRTYR1AA5255
29TYRTYRTYRTYR1BB5255
110LYSLYSLYSLYS3AA5356
210LYSLYSLYSLYS3BB5356
111PHEPHETRPTRP1AA54 - 5757 - 60
211PHEPHETRPTRP1BB54 - 5757 - 60
112VALVALVALVAL5AA5861
212VALVALVALVAL5BB5861
113PROPROPROPRO1AA6063
213PROPROPROPRO1BB6063
114ASNASNASNASN3AA6164
214ASNASNASNASN3BB6164
115LYSLYSGLUGLU4AA62 - 6765 - 70
215LYSLYSGLUGLU4BB62 - 6765 - 70
116LYSLYSASPASP1AA68 - 7771 - 80
216LYSLYSASPASP1BB68 - 7771 - 80
117PROPROASNASN4AA86 - 8789 - 90
217PROPROASNASN4BB86 - 8789 - 90
118ARGARGMETMET1AA88 - 13491 - 137
218ARGARGMETMET1BB88 - 13491 - 137
119HISHISHISHIS3AA135138
219HISHISHISHIS3BB135138
120GLUGLULEULEU1AA136 - 139139 - 142
220GLUGLULEULEU1BB136 - 139139 - 142
121ILEILEILEILE4AA140143
221ILEILEILEILE4BB140143
122ASPASPVALVAL2AA153 - 155156 - 158
222ASPASPVALVAL2BB153 - 155156 - 158
123CYSCYSLYSLYS1AA157 - 162160 - 165
223CYSCYSLYSLYS1BB157 - 162160 - 165
124GLNGLNGLNGLN3AA163166
224GLNGLNGLNGLN3BB163166

NCS oper: (Code: given
Matrix: (-0.99929, 0.035864, 0.011852), (0.034331, 0.99324, -0.11093), (-0.015751, -0.11044, -0.99376)
Vector: 60.738, 3.1051, 86.324)

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Components

#1: Protein NO APICAL MERISTEM PROTEIN / NAM / ANAC / ABSCISIC ACID RESPONSIVE NAC


Mass: 19780.664 Da / Num. of mol.: 2 / Fragment: DNA-BINDING NAC DOMAIN, RESIDUES 1-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9C932
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNP_175697 (1-168) + EXTRA RESIDUE AT THE N-TERMINUS, ORIGINATING FROM A HIS-TAG SPACER REGION

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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: 2.4 Å3/Da / Density % sol: 30 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: Olsen, A., (2004) Acta Crystallogr.,Sect.D, 60, 112.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 %PEG40001reservoir
20.1 Mimidazole-malic acid1reservoirpH7.0
33.2-7.7 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.035
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.035 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 11476 / % possible obs: 95.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / % possible all: 89.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 89.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.857 / SU B: 9.623 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.636 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 652 5.1 %RANDOM
Rwork0.225 ---
obs0.228 12163 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 0 70 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222514
X-RAY DIFFRACTIONr_bond_other_d0.0020.022243
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.953395
X-RAY DIFFRACTIONr_angle_other_deg0.85935244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.735289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022712
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02541
X-RAY DIFFRACTIONr_nbd_refined0.1880.2406
X-RAY DIFFRACTIONr_nbd_other0.2370.22341
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.21483
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7981.51473
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52122376
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73731041
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9724.51019
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1433tight positional0.040.05
260medium positional0.370.5
107loose positional0.625
1433tight thermal0.10.5
260medium thermal0.492
107loose thermal1.7910
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.404 42
Rwork0.226 809
Refinement
*PLUS
Rfactor Rfree: 0.281 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg6.8

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