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- PDB-7nzz: Ras1 guanine nucleotide exchange factor Cdc25 (REM and catalytic ... -

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Basic information

Entry
Database: PDB / ID: 7nzz
TitleRas1 guanine nucleotide exchange factor Cdc25 (REM and catalytic domains)
ComponentsCell division control protein 25
KeywordsSIGNALING PROTEIN / Ras1 protein signal transduction / Ras-exchange motif / catalytic domain / hyphal growth
Function / homology
Function and homology information


filamentous growth of a population of unicellular organisms in response to starvation / filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth / : / guanyl-nucleotide exchange factor activity / cellular response to starvation / cellular response to glucose stimulus / Ras protein signal transduction / cell division / plasma membrane
Similarity search - Function
Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain ...Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Cell division control protein 25
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsManso, J.A. / Pereira, P.J.B. / Macedo-Ribeiro, S.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: Mbio / Year: 2023
Title: Pathogen-specific structural features of Candida albicans Ras1 activation complex: uncovering new antifungal drug targets
Authors: Manso, J.A. / Carabias, A. / Sarkany, Z. / de Pereda, J.M. / Pereira, P.J.B. / Macedo-Ribeiro, S.
History
DepositionMar 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 25
B: Cell division control protein 25


Theoretical massNumber of molelcules
Total (without water)109,9282
Polymers109,9282
Non-polymers00
Water2,594144
1
A: Cell division control protein 25


Theoretical massNumber of molelcules
Total (without water)54,9641
Polymers54,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell division control protein 25


Theoretical massNumber of molelcules
Total (without water)54,9641
Polymers54,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.647, 107.214, 196.896
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cell division control protein 25


Mass: 54963.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876
Gene: CDC25, CSC25, CAALFM_C303890WA, CaO19.14188, CaO19.6926
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43069
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 23% (w/v) PEG 3350, 0.25 M sodium malonate dibasic monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.45→43.22 Å / Num. obs: 38604 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 45.24 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.073 / Rrim(I) all: 0.165 / Net I/σ(I): 8.5
Reflection shellResolution: 2.454→2.496 Å / Redundancy: 5 % / Rmerge(I) obs: 1.504 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1893 / CC1/2: 0.454 / Rpim(I) all: 0.75 / Rrim(I) all: 1.685 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROC1.05 (20190607)data processing
PHENIX1.19.1_4122refinement
XDSVERSION MAR 15, 2019 BUILT=20190806data reduction
AimlessVersion 0.7.4data scaling
CootVersion 0.9model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4US0

4us0


Resolution: 2.45→43.22 Å / SU ML: 0.3175 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9587
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 1953 5.07 %
Rwork0.1943 36579 -
obs0.1967 38532 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.56 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 0 144 6840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00196880
X-RAY DIFFRACTIONf_angle_d0.43939340
X-RAY DIFFRACTIONf_chiral_restr0.03561029
X-RAY DIFFRACTIONf_plane_restr0.00321195
X-RAY DIFFRACTIONf_dihedral_angle_d10.65592520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.520.34871470.29352490X-RAY DIFFRACTION98.47
2.52-2.580.34521110.2792610X-RAY DIFFRACTION99.52
2.58-2.660.30741260.26042552X-RAY DIFFRACTION99.55
2.66-2.750.31281480.24652596X-RAY DIFFRACTION99.85
2.75-2.840.31511180.24282604X-RAY DIFFRACTION99.89
2.84-2.960.29711190.22532585X-RAY DIFFRACTION99.85
2.96-3.090.25121500.20062603X-RAY DIFFRACTION99.89
3.09-3.250.27281380.19332606X-RAY DIFFRACTION99.85
3.25-3.460.27111400.19232610X-RAY DIFFRACTION99.85
3.46-3.730.20421510.17462592X-RAY DIFFRACTION99.85
3.73-4.10.21421380.15782626X-RAY DIFFRACTION99.82
4.1-4.690.21071540.15662629X-RAY DIFFRACTION99.71
4.69-5.910.22331550.20232669X-RAY DIFFRACTION99.58
5.91-43.220.2041580.18432807X-RAY DIFFRACTION99.56
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)
11.51226807051.033994333320.4416037944512.302909442030.7913327025272.97649984170.0139516879472-0.111344294042-0.146702633490.159184079632-0.122969368825-0.08529991654520.0854907856816-0.08216614202310.08156108615590.3017622295040.0411956271229-0.006210933068280.4409918366060.06670519536420.330915700734-7.2408251627639.7306955064-23.4110836461
24.022810080584.860691367860.4057887297697.290585134240.4567477206130.040110454310.03359331685450.219948993197-0.8360098437890.003779687192040.29062104679-1.238114853690.100953849488-0.112801955573-0.3528252000220.5293786893720.133593321243-0.03575790926420.448406195130.007679679984350.421601858448-6.130350319511.62241441958-35.4356347535
31.173223893020.3392567367020.4762541384812.224371219970.8262239041921.452401050640.0526679262074-0.0223791870136-0.09509346192320.0716306938572-0.0102620201708-0.2123569806950.122483302829-0.065774751692-0.04909560832530.358332801633-0.05697902847090.002403841306950.5406650484310.03275905078440.306602458708-27.50850712530.731642454814-40.0512038144
40.4800575843970.3709832819840.2478306648852.205075893830.8239209676730.477896554749-0.00967007051890.1435279880140.06212848394260.06128823699930.00850919367518-0.0943311461284-0.01806474482350.0094159659979-0.01051839583180.38430425968-0.06785752728110.004983016129190.7267753259860.03310222925580.379829944395-25.346841736612.7821367156-37.7797762723
52.2515244987-0.546018174840.7363444063432.22957294462-1.307428175153.24826684353-0.1129233424450.019699176877-0.0079539774515-0.001625672149350.141773278416-0.0412159382939-0.0454252993909-0.163389260729-0.0127490604310.3073685224110.005383408338260.01781455204530.555640860922-0.02960572503980.276886325892-19.446741236651.784745157510.6111657595
62.573220291150.8021227022594.276031406390.5710694122881.024814980958.081808899370.1072096932160.6730155730710.05062524972360.0600941610707-0.143101888884-0.0137743514638-0.2475463734391.161219653120.1981352117230.563246753728-0.01101661705950.05192252085430.6439410104980.05949378024820.317477145851-17.593180518162.9747090491-28.7598220917
71.40021949131-0.3443190256480.1100635123821.940329523460.1015465085162.61356272720.0985412699038-0.02393183092660.0921127108602-0.251995555527-0.03912433699530.108925597197-0.21107921661-0.133136618729-0.04047721698540.3830832118760.0241370421609-0.01033372890640.525168956938-0.006720313654170.369113462238-37.921283826370.0770565938-29.1059947233
81.350756257140.2319325790851.105430374582.926314708030.2035473161174.82685761529-0.071531276988-0.145421959663-0.065337635035-0.02554392565340.0003528453872880.1492841566210.208413909155-0.06716569026030.02580725905140.2619240158120.02840020278820.03349279613160.5416077773120.00637556460870.375496902787-40.292296600759.1086630323-16.5297016396
96.19060089827-1.127456277-1.744411028743.737993042760.3643901865495.17586090952-0.0681465563375-0.7678892608380.09276116880480.3468712402110.1557805207050.1271523397710.506159303779-0.4764406925660.03733347951470.320670763393-0.0289416410656-0.06347672285640.715252378660.1408053309810.433370857308-36.398826724457.75492847970.171492461625
104.18328300475-1.03766347376-0.7244285729764.206305252760.04422490963342.927504201430.2548162438190.03742589607610.703541597435-0.0520876690704-0.188487203707-0.177407461968-0.5430280275040.0993087555718-0.07291854178050.458122180796-0.0253173664329-0.05137508461610.467756336676-0.01121107419680.330040098414-35.374725628777.186338848-31.9158012558
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 883 through 1030 )AA883 - 10301 - 148
22chain 'A' and (resid 1031 through 1057 )AA1031 - 1057149 - 172
33chain 'A' and (resid 1058 through 1212 )AA1058 - 1212173 - 327
44chain 'A' and (resid 1213 through 1306 )AA1213 - 1306328 - 421
55chain 'B' and (resid 883 through 1030 )BB883 - 10301 - 148
66chain 'B' and (resid 1031 through 1057 )BB1031 - 1057149 - 171
77chain 'B' and (resid 1058 through 1196 )BB1058 - 1196172 - 310
88chain 'B' and (resid 1197 through 1234 )BB1197 - 1234311 - 348
99chain 'B' and (resid 1235 through 1266 )BB1235 - 1266349 - 380
1010chain 'B' and (resid 1267 through 1305 )BB1267 - 1305381 - 419

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