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- PDB-9i2s: Velvet domain of the transcriptional regulator VeA -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9i2s
TitleVelvet domain of the transcriptional regulator VeA
ComponentsDevelopmental and secondary metabolism regulator veA
KeywordsCELL CYCLE / Sexual development / secondary metabolism / regulator / veA / velvet family
Function / homology
Function and homology information


trehalose biosynthetic process / sporulation resulting in formation of a cellular spore / nucleus / cytoplasm
Similarity search - Function
Velvet factor / Velvet domain / Velvet domain superfamily / Velvet factor / Velvet domain profile.
Similarity search - Domain/homology
Developmental and secondary metabolism regulator veA
Similarity search - Component
Biological speciesAspergillus nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNeumann, P. / Ficner, R.
Funding support1items
OrganizationGrant numberCountry
Other government
Citation
Journal: To Be Published
Title: Velvet domain of the transcriptional regulator VeA
Authors: Neumann, P. / Ficner, R.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Developmental and secondary metabolism regulator veA
B: Developmental and secondary metabolism regulator veA
C: Developmental and secondary metabolism regulator veA
D: Developmental and secondary metabolism regulator veA


Theoretical massNumber of molelcules
Total (without water)98,8564
Polymers98,8564
Non-polymers00
Water79344
1
A: Developmental and secondary metabolism regulator veA
B: Developmental and secondary metabolism regulator veA


Theoretical massNumber of molelcules
Total (without water)49,4282
Polymers49,4282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-14 kcal/mol
Surface area18660 Å2
MethodPISA
2
C: Developmental and secondary metabolism regulator veA
D: Developmental and secondary metabolism regulator veA


Theoretical massNumber of molelcules
Total (without water)49,4282
Polymers49,4282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-11 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.040, 156.080, 52.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
Developmental and secondary metabolism regulator veA / Velvet complex subunit A


Mass: 24714.033 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Velvet domain residues 1 to 224 / Source: (gene. exp.) Aspergillus nidulans (mold) / Gene: veA, ANIA_01052 / Production host: Escherichia coli (E. coli) / References: UniProt: C8VTV4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350 200 mM (NH4)2SO4 100 mM BisTris/HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.4→47.21 Å / Num. obs: 34384 / % possible obs: 98 % / Redundancy: 4.18 % / Biso Wilson estimate: 71.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.047 / Net I/σ(I): 22.93
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.4-2.51.82138790.4922.0781
2.5-2.61.08833050.71.2461
2.6-2.80.68553440.8310.7881
2.8-80.0342083010.0391
8-140.00982610.0111
14-170.0089210.0091
17-500.00710810.0091

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Processing

Software
NameVersionClassificationNB
PHENIX1.21_5207refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.21 Å / SU ML: 0.4735 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2529 1719 5 %
Rwork0.2192 32642 -
obs0.2209 34361 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.05 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5475 0 0 44 5519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00395629
X-RAY DIFFRACTIONf_angle_d0.70077618
X-RAY DIFFRACTIONf_chiral_restr0.048817
X-RAY DIFFRACTIONf_plane_restr0.00591005
X-RAY DIFFRACTIONf_dihedral_angle_d4.5766740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.47781400.41062651X-RAY DIFFRACTION97.93
2.47-2.550.45621400.4052660X-RAY DIFFRACTION98.14
2.55-2.640.45391430.39642705X-RAY DIFFRACTION97.43
2.64-2.750.39191400.34292672X-RAY DIFFRACTION98.12
2.75-2.870.37081410.32772685X-RAY DIFFRACTION98.5
2.87-3.020.34921420.30662705X-RAY DIFFRACTION98.31
3.02-3.210.34571430.28172713X-RAY DIFFRACTION98.14
3.21-3.460.25231430.22192705X-RAY DIFFRACTION97.84
3.46-3.810.22431450.2092758X-RAY DIFFRACTION98.71
3.81-4.360.23521440.18912736X-RAY DIFFRACTION97.93
4.36-5.490.18661460.15812782X-RAY DIFFRACTION98.39
5.49-47.210.22491520.2012870X-RAY DIFFRACTION96.15
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)
19.14645344078-0.52438248348-4.594881725045.5660824938-0.9190261267624.303722875720.1668676263280.5694890226410.152561858880.367580961702-0.1440489282260.046682129964-0.107884954701-0.26831871116-0.03148081298260.5799611777610.03536308384130.0334295750530.655386861859-0.04789497686440.524785773683-22.942595761412.7796958565-21.8184752641
26.120861302421.59052714706-2.425227806774.85156486055-0.3787293669613.106438169130.1591684905210.2343399557870.613541773756-0.03512807910330.1083332290810.0382704050285-0.3733393159670.157778780628-0.2659833872490.6995354866790.05624531971720.05326505044870.648333189039-0.008105697915250.518891926744-17.868658580613.5249504617-26.6476060916
32.84286345808-2.12585456897-1.371437464544.798913963042.608146733681.300714486610.2405391556880.1157613667190.2644895704-0.2877967210060.02618260378350.0708334667203-0.1229972170.26700424882-0.04380046503770.6525303041820.08787480373360.07652632030470.7109554782150.03302125599630.416112355928-23.29824560047.2470868054-26.0571806083
46.842809129030.620147527458-4.246499514143.62260433126-0.2483679769343.467633992150.182331910704-0.288194040719-0.4601553845260.604811068221-0.2551526545370.9534369205350.1419223655830.03637792448460.06015195784230.7044205112390.04069483444970.1116745436930.5867271045270.02766308326640.741659695218-33.906086668110.7174023926-11.4956822171
57.80687032397-1.35076879592-1.194357191561.24608983952.175507140153.909708546120.438680024546-0.378736831675-1.18405874836-0.81121385607-0.209173748742.484631033720.678099407556-0.853594420030.2527600630110.8055815550630.0386087021136-0.3677376398670.731067278265-0.1735012859711.25927954239-37.5906651006-8.13773919631-29.108859482
63.402309137671.578480535011.649273027493.852620273771.115985215123.44710123533-0.2670186622340.810629095601-0.426307218258-0.04215652989630.535127551203-2.062335102410.844675981342.092083707690.2922190467110.9772348322870.0732474622782-0.1480988834251.219116359290.05890699554231.05325100992-8.34556337132-13.7927624656-14.6512629697
75.14610323408-3.00841541891.48470259365.91453969241-1.805693861322.937345351090.4305605226470.492049283119-0.698998226369-1.33265444858-0.08313008726680.8631317367650.31355388882-0.143955531223-0.2385938927880.9589615787660.10215112788-0.261523227940.621728664189-0.07601363024210.687295834144-31.8241856012-10.260296939-30.0680588455
85.178387409920.1422065427810.613988942663.820245644810.1420538523324.4187700878-0.2910504389780.560552393770.6013563791230.74008133248-0.246833515329-0.154160683338-0.4268324363850.7645294258670.2696672076670.8354659912430.183432192138-0.03079689682530.443746653927-0.07912236797210.603617211765-16.8293189441-3.72209995712-16.8172853946
93.80201334177-2.010566851551.757078026026.20972920041-1.566138845896.612558269260.4054728659260.502553264572-0.124949048726-0.719825211097-0.390293712540.2416287992910.526273871091-0.13361861361-0.265956169460.7861119512370.0640149464765-0.003128759519320.620345453249-0.02944936715050.592722083003-22.5678617028-10.1990555971-25.4685131382
107.401595197530.153950447474-0.2012684008724.153553841672.037046167053.297031718871.960984653072.717708512940.164703818652-1.7785605938-0.983633743610.992559542741.27983907067-0.0337313900992-0.95621927112.417099230120.411629939645-0.3896699257471.86239380654-0.1122956962731.25557748889-33.19736666934.30550089951-40.0340172295
112.71840800903-0.586795696412.604970681895.3742963096-2.061421754913.119053074350.235724380049-0.5509996012820.2033123139960.536776092164-0.101447562668-0.767807068685-0.00706812312237-0.1387803929020.1765140792240.7753704627170.0823848599211-0.08900724854570.700652628566-0.06681872356780.613920662722-15.2559436065-10.2706678633-13.8545291495
121.076882029330.09708424356520.2232532535457.04532328396.30962219129.32835978616-0.1829370570930.2805405484590.621060190705-0.751159197493-0.1342228307490.750799361538-0.6861454995380.4794148282570.2703640720150.8961515028980.0329307005285-0.09434233959720.810090220092-0.0584102193690.71100466636-54.705187723546.9441510002-13.4922023576
132.54651413071-0.301048253978-0.2972555622281.91388877555-0.02431560886540.226718583457-0.0455034332158-1.32407964947-0.8346052636161.050123768460.314987939855-0.220827380770.4917461512580.195887671086-0.2397120133870.948887597474-0.01461989801870.01147264291561.05748097418-0.1971614095941.264235994-41.704709588552.882767618516.9040031977
144.483528514430.351950605347-1.183136841992.83656436908-0.3922862360414.31302692785-0.0653100329748-0.1954661965430.117951496565-0.1310308939250.01144360852610.902668426767-0.379277774183-0.139961693839-0.2724634539470.7117189128940.0558016292232-0.1220446872820.618929561762-0.07540834196320.79845483912-52.367075654153.21931922050.484467934366
151.707597560170.6701024421841.973665726094.80593553536-1.102051894696.183758246390.120740007460.478566476411-0.370449125208-1.083863924540.3175306262580.5649824649590.119212503587-0.215542786006-0.2314449918540.783271265873-0.037913397984-0.1517250088840.78814156745-0.05929079021840.638848142555-57.269747826447.4739862534-11.0962315409
161.464883187150.877002457022-1.07199895634.191847045041.32774448795.455939142110.672676789118-0.288599195683-0.2789739310420.0856964209249-0.137691914021-0.551219000337-0.422882337780.761174014626-0.5738955078120.717325655512-0.04271566823190.0607147594310.82732051351-0.04316198735460.951958464151-43.497941119842.53999345038.65963668924
172.6303471324-0.2967509511331.905618275715.47349998216-0.6353007785917.55076268645-0.102770732588-0.08233429998980.00332461041551-0.2395091917180.03452856594950.6476467866180.0289917061111-0.73042474581-0.07759708160730.496561823309-0.00248775839369-0.09003255370310.651265714953-0.08239951323840.642519201683-55.771562018246.5390792587-0.864039832042
184.246185603311.671679749623.670184988473.527189775490.4261964851685.50682929606-0.187160085750.1894447840710.1128531228310.1170754552930.0663884271972-0.255863304996-0.2940488826370.633173780660.04144802136680.6003457167010.04889930057620.01088711593950.651537066777-0.04218194595750.862058197376-41.8824177149.685332954810.1312164529
192.217626206590.9310455378253.159264303382.033468583941.234700191964.4278549808-0.262925057279-1.2041723039-0.2652236473841.40073615962-0.1625691594170.5351750585710.6687048205120.07739148856230.2431086054511.11530569696-0.1013659770110.4708216233350.9062988903670.02428299119530.918648901278-55.43156972728.191531604314.6004129334
204.9604619181.80591191812-0.6161511730934.051579670591.662817409873.467824692880.2382309814741.192682541570.442986964457-0.9998976670640.7982871289690.67615393533-0.402468273059-1.25914055912-0.04134861302291.228783267180.1979086958060.1990184613040.9165601438120.05981373630671.08385664549-38.821886580927.8156343009-12.7751519341
215.58080158683-0.1506593629321.160506546564.960981529290.6749168733725.122843901340.145859775331-0.60792418249-0.680437088790.186343224298-0.5753416602050.3815702447070.9705975717910.4048137649770.1748775904710.692980207494-0.1123996407650.2091600254240.6449131683630.004520106881780.902791886672-50.652194978523.50942110520.571308813965
221.778891604990.704911394033-0.6120893514493.17940757191-0.3918205145040.202948460087-0.370276698413-0.452037402645-1.147002237380.969485835946-0.3134651391280.2670754009080.638262299003-0.192861005819-2.271053343630.778870228193-0.2539785398251.252008781141.16006642540.2937477772451.64709136495-62.351532689523.222679987218.9780116762
234.11096765082-2.196885992690.2753053545736.80997358691-0.3840233570944.47367710242-0.255003614621-0.188492919312-0.419968646084-0.09507775512950.01595375570360.7052041580830.746628610517-0.195396192590.09925773737430.5594956669340.05167083908940.06920295887610.695633982766-0.1251369885910.621964404865-50.445690713228.56130830770.0349681944523
243.35725245675-0.650909637013-0.6668251862877.179744348412.121486490955.7514492287-0.186552190216-0.0459290133893-0.487387199986-0.0615801337539-0.1397975975440.459574135380.00939037594512-0.1318502359030.1088954195080.422223866317-0.01282006545810.03362969491910.611315921454-0.01873812802230.644702063751-47.901506994329.7927761696-1.5785959419
253.46514945261.28854408834-0.7733354389566.36406927421-0.5220813531624.65802952884-0.378055571067-0.323345715594-0.09921651795620.879748401660.02452264389581.056348771440.214735890901-0.8060240124650.1338148937650.676323506086-0.07631017287710.1263486003190.866984204767-0.08187083181970.881460506366-54.772349116633.783511115.56125534717
261.89290302448-1.62690970586-3.217532680623.80155665591.771065403695.858062116230.6342486313481.20996138519-0.600486055369-1.905001522020.636772476010.416339471481-0.49021651848-0.3072032077110.02770388346861.571250176820.2335429083150.3177437870521.089676167920.04685807105581.30616429529-29.027554263925.7851395796-24.3243748964
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 72 )AA15 - 721 - 58
22chain 'A' and (resid 73 through 133 )AA73 - 13359 - 106
33chain 'A' and (resid 134 through 188 )AA134 - 188107 - 145
44chain 'A' and (resid 189 through 212 )AA189 - 212146 - 169
55chain 'B' and (resid 15 through 38 )BB15 - 381 - 24
66chain 'B' and (resid 39 through 56 )BB39 - 5625 - 40
77chain 'B' and (resid 57 through 99 )BB57 - 9941 - 83
88chain 'B' and (resid 100 through 124 )BB100 - 12484 - 97
99chain 'B' and (resid 125 through 160 )BB125 - 16098 - 133
1010chain 'B' and (resid 161 through 187 )BB161 - 187134 - 144
1111chain 'B' and (resid 188 through 212 )BB188 - 212145 - 169
1212chain 'C' and (resid 15 through 38 )CC15 - 381 - 24
1313chain 'C' and (resid 39 through 53 )CC39 - 5325 - 39
1414chain 'C' and (resid 54 through 73 )CC54 - 7340 - 59
1515chain 'C' and (resid 74 through 99 )CC74 - 9960 - 85
1616chain 'C' and (resid 100 through 124 )CC100 - 12486 - 101
1717chain 'C' and (resid 125 through 187 )CC125 - 187102 - 148
1818chain 'C' and (resid 188 through 212 )CC188 - 212149 - 173
1919chain 'D' and (resid 15 through 38 )DD15 - 381 - 24
2020chain 'D' and (resid 39 through 53 )DD39 - 5325 - 39
2121chain 'D' and (resid 54 through 73 )DD54 - 7340 - 59
2222chain 'D' and (resid 74 through 88 )DD74 - 8860 - 74
2323chain 'D' and (resid 89 through 133 )DD89 - 13375 - 108
2424chain 'D' and (resid 134 through 160 )DD134 - 160109 - 135
2525chain 'D' and (resid 161 through 202 )DD161 - 202136 - 161
2626chain 'D' and (resid 203 through 212 )DD203 - 212162 - 171

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