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- PDB-4n6q: Crystal structure of VosA velvet domain -

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Basic information

Entry
Database: PDB / ID: 4n6q
TitleCrystal structure of VosA velvet domain
ComponentsVosA
KeywordsDNA BINDING PROTEIN / Ig-fold / NFKB / beta-sandwich / transcription factor / VelB
Function / homology
Function and homology information


conidium formation / trehalose biosynthetic process / sporulation resulting in formation of a cellular spore / identical protein binding / nucleus
Similarity search - Function
Velvet domain / Velvet factor / Velvet domain / Velvet domain superfamily / Velvet factor / Velvet domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / NITRATE ION / Spore development regulator vosA / Spore development regulator vosA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.79 Å
AuthorsAhmed, Y.L. / Dickmanns, A. / Neumann, P. / Ficner, R.
CitationJournal: Plos Biol. / Year: 2013
Title: The Velvet Family of Fungal Regulators Contains a DNA-Binding Domain Structurally Similar to NF-kappa B.
Authors: Ahmed, Y.L. / Gerke, J. / Park, H.S. / Bayram, O. / Neumann, P. / Ni, M. / Dickmanns, A. / Kim, S.C. / Yu, J.H. / Braus, G.H. / Ficner, R.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: VosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0966
Polymers22,5921
Non-polymers5055
Water3,459192
1
A: VosA
hetero molecules

A: VosA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,19312
Polymers45,1832
Non-polymers1,00910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area3560 Å2
ΔGint-20 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 45.400, 189.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-305-

NO3

21A-305-

NO3

31A-582-

HOH

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Components

#1: Protein VosA


Mass: 22591.584 Da / Num. of mol.: 1 / Fragment: velvet domain (UNP residues 1-190)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Plasmid: pETM13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: A0SP16, UniProt: Q5BBX1*PLUS
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES, pH 6.5, 32% PEG 2000 MME, 150 mM KI, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 13, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 142535 / Rmerge(I) obs: 0.036 / D res high: 1.79 Å / Num. obs: 35476 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
5.66872110010.024
4.625.6695010010.026
44.62113210010.025
3.584127199.910.027
3.273.58138899.810.029
3.023.27152299.910.03
2.833.02164710010.033
2.672.83171699.910.037
2.532.67185699.710.039
2.412.53194599.910.045
2.312.41202699.810.052
2.222.31214299.910.059
2.142.22219099.710.066
2.072.14223599.710.078
22.07238999.910.092
1.942243799.810.118
1.891.94247599.810.166
1.841.89260299.910.233
1.791.8424409210.286
ReflectionResolution: 1.79→32.1 Å / Num. obs: 19471 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.01 % / Biso Wilson estimate: 28.917 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.042 / Net I/σ(I): 22.17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.79-1.840.2864.6481322440192
1.84-1.890.2335.9698002602199.9
1.89-1.940.1667.9893612475199.8
1.94-20.11810.6292722437199.8
2-2.070.09213.0691352389199.9
2.07-2.140.07815.2886792235199.7
2.14-2.220.06617.9285822190199.7
2.22-2.310.05920.1885152142199.9
2.31-2.410.05222.9382242026199.8
2.41-2.530.04525.7181271945199.9
2.53-2.670.03930.3179761856199.7
2.67-2.830.03732.8574091716199.9
2.83-3.020.03336.51712716471100
3.02-3.270.0341.0665951522199.9
3.27-3.580.02943.6460171388199.8
3.58-40.02746.3355421271199.9
4-4.620.02547.4494411321100
4.62-5.660.02648.6841849501100
5.66-80.02447.4731997211100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→32.1 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8839 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0.03 / σ(I): 0 / Phase error: 17.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 976 5.01 %RANDOM
Rwork0.1833 ---
obs0.1851 19471 98.67 %-
all-19471 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.822 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 87.87 Å2 / Biso mean: 27.1545 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.2009 Å2-0 Å20 Å2
2---0.2009 Å20 Å2
3---0.4018 Å2
Refinement stepCycle: LAST / Resolution: 1.79→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 11 192 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131453
X-RAY DIFFRACTIONf_angle_d1.5671965
X-RAY DIFFRACTIONf_chiral_restr0.109213
X-RAY DIFFRACTIONf_plane_restr0.009260
X-RAY DIFFRACTIONf_dihedral_angle_d13.842552
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.79-1.88390.34181290.26092448257794
1.8839-2.00190.22611360.17742560269698
2.0019-2.15640.22581380.16582605274399
2.1564-2.37330.22161390.1782611275099
2.3733-2.71660.24971400.184626572797100
2.7166-3.4220.21581420.179627032845100
3.422-32.10780.19251520.182229113063100
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)
10.26780.23360.11710.09690.26670.39940.0016-0.02850.1272-0.047-0.04460.0787-0.2113-0.11430.00190.15730.0549-0.02680.20010.05930.18617.673112.7597-8.4887
20.3622-0.40390.11540.5691-0.08930.09870.285-0.2886-0.3350.17810.06020.21270.08340.04950.04510.1589-0.0312-0.03670.3850.00910.110114.418-2.85318.3397
30.04560.1013-0.06230.2375-0.07830.1406-0.1307-0.3353-0.8410.06060.0613-0.09040.2660.2630.0070.17860.0479-0.05890.34860.1430.253117.9307-6.272814.9881
40.2520.29740.06010.4513-0.15230.1929-0.07930.11890.3063-0.09950.24040.15670.1072-0.2080.05850.09240.0074-0.02810.24210.07270.18418.70857.564-10.7335
50.36690.0938-0.03890.0364-0.20030.2621-0.0649-0.10090.19150.0860.03120.0024-0.13440.000100.14880.0339-0.00060.2137-0.03260.162613.598812.289111.8579
60.34140.11-0.33230.2772-0.02450.28310.05290.0423-0.02880.0155-0.0223-0.00510.05520.0865-0.00010.10820.0096-0.01240.1944-0.00250.110513.61090.44341.4836
70.37670.18580.18090.29520.13810.33220.0138-0.01930.0239-0.0341-0.0372-0.0591-0.0221-0.0131-0.0010.08850.01620.00310.1423-0.0030.104114.91398.25324.1806
80.16520.16580.02260.1003-0.02090.21920.3356-0.1692-0.2872-0.0299-0.00620.00050.2567-0.24410.00610.1947-0.0504-0.06560.24760.0430.17399.6845-1.771820.8194
90.0237-0.03490.00170.09860.03680.03570.14040.0002-0.20720.1153-0.1886-0.24180.4376-0.24580.00030.1763-0.0223-0.02250.187-0.00350.15936.4624-10.24713.5236
100.0137-0.01240.03040.0855-0.06730.0426-0.1493-0.0446-0.1733-0.1182-0.0494-0.3280.35780.64710.0010.22640.11850.01940.40520.03060.232913.6076-11.11623.6121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 8:26)A8 - 26
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 27:37)A27 - 37
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 38:47)A38 - 47
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 48:70)A48 - 70
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 71:89)A71 - 89
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 90:111)A90 - 111
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 112:150)A112 - 150
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 151:166)A151 - 166
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 167:176)A167 - 176
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 177:185)A177 - 185

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