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- PDB-4n6r: Crystal structure of VosA-VelB-complex -

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Basic information

Entry
Database: PDB / ID: 4n6r
TitleCrystal structure of VosA-VelB-complex
Components
  • VelB
  • VosA
KeywordsDNA BINDING PROTEIN/transcription / Ig-fold / transcription factor / DNA BINDING PROTEIN-transcription complex
Function / homology
Function and homology information


positive regulation of sterigmatocystin biosynthetic process / positive regulation of sexual sporulation resulting in formation of a cellular spore / sterigmatocystin biosynthetic process / negative regulation of conidium formation / conidium formation / sexual sporulation resulting in formation of a cellular spore / trehalose biosynthetic process / cellular response to light stimulus / sporulation resulting in formation of a cellular spore / identical protein binding ...positive regulation of sterigmatocystin biosynthetic process / positive regulation of sexual sporulation resulting in formation of a cellular spore / sterigmatocystin biosynthetic process / negative regulation of conidium formation / conidium formation / sexual sporulation resulting in formation of a cellular spore / trehalose biosynthetic process / cellular response to light stimulus / sporulation resulting in formation of a cellular spore / identical protein binding / nucleus / cytoplasm
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
Spore development regulator vosA / Velvet complex subunit B / Velvet complex subunit B / Spore development regulator vosA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: VelB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7513
Polymers63,6552
Non-polymers961
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-36 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.030, 56.750, 138.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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): Rosetta 2 (DE3) / References: UniProt: A0SP16, UniProt: Q5BBX1*PLUS
#2: Protein VelB


Mass: 41063.832 Da / Num. of mol.: 1
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): Rosetta 2 (DE3) / References: UniProt: A5HMG5, UniProt: C8VTS4*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 4000, 150 mM (NH4)2SO4, 100 mM MES, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→37.142 Å / Num. all: 20664 / Num. obs: 20664 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 26.334 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.138 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.324.50.4651.61341829810.46598.3
2.32-2.464.50.3422.21288828710.34298.1
2.46-2.634.50.2652.91205726710.26597.8
2.63-2.844.50.1913.91125724930.19197.5
2.84-3.114.50.1335.61030322720.13397.1
3.11-3.484.60.0868.1947520810.08696.4
3.48-4.024.50.0847.8830618330.08496
4.02-4.924.50.0896.9695715440.08995.6
4.92-6.964.50.0816.7544912190.08194.8
6.96-38.3514.20.069.429156990.0692.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.41 / Model details: Phaser MODE: MR_AUTO / Packing: 0
Highest resolutionLowest resolution
Rotation2.2 Å29.62 Å
Translation2.2 Å29.62 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N6Q

4n6q


Resolution: 2.2→36.954 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8712 / SU ML: 0.7 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1017 4.93 %RANDOM
Rwork0.19 ---
obs0.1926 20631 96.09 %-
all-20631 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.729 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 147.85 Å2 / Biso mean: 25.8134 Å2 / Biso min: 0.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.9293 Å20 Å20 Å2
2--3.0579 Å20 Å2
3---5.0916 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 5 251 3004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032855
X-RAY DIFFRACTIONf_angle_d0.7373882
X-RAY DIFFRACTIONf_chiral_restr0.051435
X-RAY DIFFRACTIONf_plane_restr0.003506
X-RAY DIFFRACTIONf_dihedral_angle_d13.181066
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 (%)
2.2-2.3160.28441430.22022764290798
2.316-2.46110.29751460.21092821296798
2.4611-2.6510.26751420.20482778292097
2.651-2.91770.25771450.19922799294497
2.9177-3.33970.26231500.18422792294296
3.3397-4.20670.21921410.17012793293495
4.2067-36.95920.21231500.18612867301793
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)
10.7453-0.1003-0.19790.98040.24820.8439-0.0044-0.0912-0.11820.04770.01580.06110.146-0.0347-0.02780.0458-0.00950.00660.0140.01790.0482-0.7238-13.6919-21.9078
20.9861-0.05370.22011.03160.00890.93470.0164-0.15080.03540.110.0517-0.1068-0.07110.12520.42110.0045-0.034-0.0028-0.01220.0057-0.00115.416-2.0316-18.6137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA7 - 160
2X-RAY DIFFRACTION2CHAIN BB44 - 343

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