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Basic information

Entry
Database: PDB / ID: 2ntx
TitleProne8
ComponentsEmb|CAB41934.1
KeywordsSIGNALING PROTEIN / dimer / guanine nucleotide exchange factor
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity / identical protein binding / plasma membrane
Similarity search - Function
PRONE domain, subdomain 2 / PRONE domain, subdomain 1 / PRONE domain / Rop guanine nucleotide exchange factor / PRONE (Plant-specific Rop nucleotide exchanger) / PRONE domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsThomas, C. / Fricke, I. / Scrima, A. / Berken, A. / Wittinghofer, A.
Citation
Journal: Mol.Cell / Year: 2007
Title: Structural Evidence for a Common Intermediate in Small G Protein-GEF Reactions
Authors: Thomas, C. / Fricke, I. / Scrima, A. / Berken, A. / Wittinghofer, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Purification and crystallization of the catalytic PRONE domain of RopGEF8 and its complex with Rop4 from Arabidopsis thaliana
Authors: Thomas, C. / Weyand, M. / Wittinghofer, A. / Berken, A.
History
DepositionNov 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Emb|CAB41934.1
B: Emb|CAB41934.1


Theoretical massNumber of molelcules
Total (without water)84,3462
Polymers84,3462
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-22 kcal/mol
Surface area30400 Å2
MethodPISA
2
A: Emb|CAB41934.1
B: Emb|CAB41934.1

A: Emb|CAB41934.1
B: Emb|CAB41934.1


Theoretical massNumber of molelcules
Total (without water)168,6924
Polymers168,6924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area8130 Å2
ΔGint-58 kcal/mol
Surface area57930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.339, 114.339, 318.964
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Emb|CAB41934.1 / PRONE8


Mass: 42172.895 Da / Num. of mol.: 2 / Fragment: UNP residues 76-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: At3g24620 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9LV40
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 740mM NaCl, 100mM sodium citrate, pH 5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9793
SYNCHROTRONSLS X10SA20.8985
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDAug 27, 2005
MARMOSAIC 225 mm CCD2CCDAug 27, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.89851
ReflectionAv σ(I) over netI: 17.28 / Number: 366548 / Rmerge(I) obs: 0.076 / D res high: 2.8 Å / Num. obs: 54359 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obs
2.82.997.610.396
2.9399.810.372
33.199.910.329
3.13.299.710.282
3.23.399.710.228
3.3499.810.125
4599.910.061
5610010.053
ReflectionResolution: 2.2→20 Å / Num. obs: 62938 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.98
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.2-2.30.4524.250045741795.9
2.3-2.40.3865.756635651499.9
2.4-2.50.3427.663484554599.9
2.5-2.60.30810.172010473699.9
2.6-2.80.23413.9129432757099.9
2.8-30.16518.697023569699.8
3-3.30.10925.5105090618799.7
3.3-3.80.06836.2109732652199.9
3.8-4.50.0534482277497199.9
4.5-5.50.0641554973472100
5.5-70.0640.6343142205100
7-90.04150.916808113899.1
9-120.03652.8805660099
12-150.03750.1277722897.9
150.03747.1155713892

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.819.800251684877
ANO_12.819.81.550250090
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_110.66-19.800302247
ISO_18.15-10.6600506237
ISO_16.85-8.1500652258
ISO_16.02-6.8500767244
ISO_15.44-6.0200870245
ISO_15-5.4400979250
ISO_14.65-5001053232
ISO_14.36-4.65001146249
ISO_14.12-4.36001218237
ISO_13.92-4.12001297239
ISO_13.75-3.92001353239
ISO_13.59-3.75001441225
ISO_13.45-3.59001498242
ISO_13.33-3.45001561243
ISO_13.22-3.33001598247
ISO_13.12-3.22001702250
ISO_13.03-3.12001719258
ISO_12.95-3.03001792249
ISO_12.87-2.95001839243
ISO_12.8-2.87001875243
ANO_110.66-19.86.31903020
ANO_18.15-10.666.57905060
ANO_16.85-8.156.49506520
ANO_16.02-6.855.81307670
ANO_15.44-6.025.09108700
ANO_15-5.444.08809790
ANO_14.65-53.345010530
ANO_14.36-4.652.702011460
ANO_14.12-4.362.088012180
ANO_13.92-4.121.746012970
ANO_13.75-3.921.413013530
ANO_13.59-3.751.14014410
ANO_13.45-3.590.87014980
ANO_13.33-3.450.676015610
ANO_13.22-3.330.624015980
ANO_13.12-3.220.489017020
ANO_13.03-3.120.377017190
ANO_12.95-3.030.309017920
ANO_12.87-2.950.252018060
ANO_12.8-2.870.202017490
Phasing dmFOM : 0.92 / FOM acentric: 0.92 / FOM centric: 0.92 / Reflection: 30332 / Reflection acentric: 25253 / Reflection centric: 5079
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-19.7980.980.980.981382857525
5-80.950.960.9442053215990
4-50.960.960.9651324211921
3.5-40.940.940.9551054325780
3-3.50.90.90.89900277951207
2.8-30.860.860.8455064850656

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
RESOLVE2.05phasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.74 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.891 / SU B: 10.417 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 3146 5 %RANDOM
Rwork0.24362 ---
obs0.24496 59790 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 0 174 4793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224709
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9776378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.1445608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06824.921189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.61515847
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3511525
X-RAY DIFFRACTIONr_chiral_restr0.140.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023460
X-RAY DIFFRACTIONr_nbd_refined0.210.22187
X-RAY DIFFRACTIONr_nbtor_refined0.2930.23315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3120.2197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.8760.211
X-RAY DIFFRACTIONr_mcbond_it0.6241.53105
X-RAY DIFFRACTIONr_mcangle_it0.89824833
X-RAY DIFFRACTIONr_scbond_it1.76231817
X-RAY DIFFRACTIONr_scangle_it2.6934.51540
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 213 -
Rwork0.276 4049 -
obs-4262 100 %
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)
10.70270.11-0.41781.6589-0.18281.0516-0.0042-0.0624-0.0017-0.0308-0.0004-0.2156-0.05230.14420.0046-0.11570.03580.0102-0.0428-0.0095-0.10819.1891-49.7823-42.0559
21.3918-1.1324-0.60271.31280.52281.44450.00520.0931-0.1810.0453-0.07070.21540.0907-0.25450.0655-0.0981-0.01710.0348-0.06220.0069-0.0808-29.3202-38.4301-17.2237
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA7 - 3627 - 362
22BB3 - 3563 - 356

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