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- PDB-6c87: Crystal structure of rab gdp dissociation inhibitor alpha from Na... -

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Basic information

Entry
Database: PDB / ID: 6c87
TitleCrystal structure of rab gdp dissociation inhibitor alpha from Naegleria fowleri
ComponentsRab GDP dissociation inhibitor alpha
KeywordsPROTEIN TRANSPORT / SSGCID / Structural Genomics / Naegleria fowleri / rab gdp dissociation inhibitor alpha / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Rab GDP-dissociation inhibitor activity / small GTPase-mediated signal transduction / protein transport
Similarity search - Function
Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Rab GDI protein / Guanine Nucleotide Dissociation Inhibitor; domain 2 / Guanine Nucleotide Dissociation Inhibitor, domain 2 / GDP dissociation inhibitor / GDP dissociation inhibitor / Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rab GDP dissociation inhibitor
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of rab gdp dissociation inhibitor alpha from Naegleria fowleri
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rab GDP dissociation inhibitor alpha
B: Rab GDP dissociation inhibitor alpha
C: Rab GDP dissociation inhibitor alpha
D: Rab GDP dissociation inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,9776
Polymers204,7854
Non-polymers1922
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.340, 103.120, 195.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 60 or (resid 61...
21(chain B and (resid 1 through 3 or (resid 4...
31(chain C and (resid 1 through 52 or (resid 53...
41(chain D and (resid 1 through 52 or (resid 53...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resid 1 through 60 or (resid 61...AA1 - 609 - 68
12LYSLYSLYSLYS(chain A and (resid 1 through 60 or (resid 61...AA6169
13METMETGLNGLN(chain A and (resid 1 through 60 or (resid 61...AA1 - 4429 - 450
14METMETGLNGLN(chain A and (resid 1 through 60 or (resid 61...AA1 - 4429 - 450
15METMETGLNGLN(chain A and (resid 1 through 60 or (resid 61...AA1 - 4429 - 450
16METMETGLNGLN(chain A and (resid 1 through 60 or (resid 61...AA1 - 4429 - 450
21METMETGLUGLU(chain B and (resid 1 through 3 or (resid 4...BB1 - 39 - 11
22GLUGLUGLUGLU(chain B and (resid 1 through 3 or (resid 4...BB412
23METMETSO4SO4(chain B and (resid 1 through 3 or (resid 4...BB - F1 - 5009
24METMETSO4SO4(chain B and (resid 1 through 3 or (resid 4...BB - F1 - 5009
25METMETSO4SO4(chain B and (resid 1 through 3 or (resid 4...BB - F1 - 5009
26METMETSO4SO4(chain B and (resid 1 through 3 or (resid 4...BB - F1 - 5009
31METMETPHEPHE(chain C and (resid 1 through 52 or (resid 53...CC1 - 529 - 60
32GLUGLUGLUGLU(chain C and (resid 1 through 52 or (resid 53...CC5361
33METMETPROPRO(chain C and (resid 1 through 52 or (resid 53...CC1 - 4419 - 449
34METMETPROPRO(chain C and (resid 1 through 52 or (resid 53...CC1 - 4419 - 449
35METMETPROPRO(chain C and (resid 1 through 52 or (resid 53...CC1 - 4419 - 449
36METMETPROPRO(chain C and (resid 1 through 52 or (resid 53...CC1 - 4419 - 449
41METMETPHEPHE(chain D and (resid 1 through 52 or (resid 53...DD1 - 529 - 60
42GLUGLUGLUGLU(chain D and (resid 1 through 52 or (resid 53...DD5361
43METMETPROPRO(chain D and (resid 1 through 52 or (resid 53...DD1 - 4419 - 449
44METMETPROPRO(chain D and (resid 1 through 52 or (resid 53...DD1 - 4419 - 449
45METMETPROPRO(chain D and (resid 1 through 52 or (resid 53...DD1 - 4419 - 449
46METMETPROPRO(chain D and (resid 1 through 52 or (resid 53...DD1 - 4419 - 449

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Components

#1: Protein
Rab GDP dissociation inhibitor alpha


Mass: 51196.320 Da / Num. of mol.: 4 / Fragment: NafoA.19251.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Strain: ATCC 30863 / Gene: NF0049320 / Plasmid: NafoA.01385.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A2R2JFX6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Rigaku Reagents JCSG+ screen E1: 1000 mM Sodium citrate tribasic, 100mM Na cacodylate / HCl pH 6.5 : NafoA.01385.a.B1 at 21.13mg/ml: cryo: 20% EG: tray 295598 E1: puck meu4-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→47.95 Å / Num. obs: 61169 / % possible obs: 99.8 % / Redundancy: 6.228 % / Biso Wilson estimate: 45.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.081 / Χ2: 1.033 / Net I/σ(I): 19.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.676.3070.5453.4244710.890.594100
2.67-2.746.3150.4464.1543530.9180.486100
2.74-2.826.3020.3685.1142340.9450.40199.9
2.82-2.916.3120.3036.1641410.9590.331100
2.91-36.3040.2537.3240030.9720.276100
3-3.116.2950.1969.1838640.9840.214100
3.11-3.226.2760.15111.8637750.9890.165100
3.22-3.366.2910.11715.2136000.9930.12899.9
3.36-3.516.2720.08919.2434520.9960.09799.9
3.51-3.686.2370.07222.8333160.9970.07899.8
3.68-3.886.2560.05827.331600.9980.063100
3.88-4.116.2180.04931.3730040.9980.05399.6
4.11-4.396.2180.04236.5228040.9990.04699.8
4.39-4.756.1720.03839.3126370.9990.04199.7
4.75-5.26.1620.03838.6524330.9990.04299.6
5.2-5.816.1380.03936.9822070.9990.04399.5
5.81-6.716.0650.03936.5219700.9990.04399.6
6.71-8.225.9650.03143.316710.9990.03499.4
8.22-11.635.8440.02450.1613220.9990.02699
11.63-47.955.1580.02546.947520.9990.02895.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
SIMBADphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3cpi chain G as per Morda, target identified with SIMBAD

3cpi


Resolution: 2.6→47.95 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.47
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 1937 3.17 %0
Rwork0.1719 ---
obs0.1734 61129 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.28 Å2 / Biso mean: 52.4132 Å2 / Biso min: 1.75 Å2
Refinement stepCycle: final / Resolution: 2.6→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13406 0 10 396 13812
Biso mean--103.74 42.52 -
Num. residues----1765
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7934X-RAY DIFFRACTION8.734TORSIONAL
12B7934X-RAY DIFFRACTION8.734TORSIONAL
13C7934X-RAY DIFFRACTION8.734TORSIONAL
14D7934X-RAY DIFFRACTION8.734TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.66510.33491310.24341744305100
2.6651-2.73710.28021340.217541724306100
2.7371-2.81760.27581630.204441534316100
2.8176-2.90860.24751620.193641794341100
2.9086-3.01250.26121500.241704320100
3.0125-3.13310.24831340.210342364370100
3.1331-3.27570.30131270.204241814308100
3.2757-3.44830.25271410.190942254366100
3.4483-3.66430.23511400.175741974337100
3.6643-3.94710.2221400.164442374377100
3.9471-4.34410.20181430.145142294372100
4.3441-4.97210.16811420.132442544396100
4.9721-6.26210.24051200.159943214441100
6.2621-47.95790.14041100.15754464457498
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)
11.92990.6677-0.05682.8536-0.03461.48980.033-0.09210.3375-0.0265-0.09350.0427-0.2435-0.01920.05860.2262-0.00580.0310.25520.02250.2947-13.193876.6022112.3254
22.54070.280.83941.85380.46541.2531-0.22530.15980.4596-0.411-0.01170.2113-0.3-0.21790.15870.4020.0763-0.02560.37810.06210.372749.122371.7926124.9934
32.0040.39630.46951.38480.40451.15780.06660.11760.0607-0.17530.0633-0.184-0.02550.076-0.02720.33740.0510.06250.33320.00580.380862.352962.3728133.414
41.908-0.15521.00271.9832-0.18833.1067-0.04110.3229-0.0858-0.0442-0.04230.04770.05720.27060.01640.32950.01210.02340.2735-0.04410.366650.114850.7695131.5992
52.7433-0.5136-0.93612.0219-0.71083.1824-0.04350.085-0.6092-0.16840.11090.51870.5598-1.1094-0.21080.6124-0.2512-0.04770.69080.0810.606737.064137.2548147.6626
65.09310.1702-1.833.0822-0.59915.54430.33140.4294-0.11460.03110.13480.44420.0934-1.051-0.27610.4049-0.0616-0.01250.51860.10030.429438.708645.7157139.6884
72.5556-0.02140.23941.59080.13942.55620.08280.38660.1176-0.5166-0.243-0.0373-0.0170.11950.08350.44290.09010.00660.38370.01780.288352.401558.2158123.9107
81.5709-1.83890.0732.1354-0.15210.0721-0.1040.15110.8011-0.70710.07740.2443-1.0457-0.3570.19120.92710.1618-0.01040.71230.08590.799439.717982.2416121.0279
91.6288-0.35360.26921.8668-0.1251.9385-0.09140.00210.16530.09070.05490.2081-0.1006-0.25970.00670.32870.07590.03750.30850.01530.303348.620262.2015138.3766
104.2866-1.094-1.76071.19750.33771.7026-0.04990.5191-0.4215-0.2376-0.12380.06110.2013-0.02860.20650.39590.0579-0.01070.3514-0.03280.3097-7.261132.2648127.7395
112.1598-0.4316-1.84992.64221.13892.47690.3707-0.19840.7031-0.04870.1225-0.7108-0.34030.6335-0.43560.4471-0.06640.06780.4127-0.04660.61714.250960.7091139.7293
122.1431-0.7799-0.54472.15780.57891.3315-0.06420.02750.0662-0.01650.0728-0.21040.13650.2014-0.00760.30720.0702-0.02470.29990.00090.2354-1.77339.564135.834
131.74220.66911.88533.40911.07912.13410.06061.5240.4491-0.6346-0.1712-0.52220.1564-0.11350.00280.43710.06770.08760.67360.11980.434411.557440.9773122.8541
142.48181.0065-0.49692.1732-0.39881.81330.0933-0.2212-0.47340.2697-0.0776-0.30570.49330.09540.00830.4715-0.0574-0.07040.2669-0.010.335164.827929.772116.7432
151.9882-0.2178-0.04471.6319-0.61861.85910.0653-0.03930.1176-0.0510.14480.46960.2852-0.9071-0.21090.3837-0.1796-0.00570.61420.04140.424942.76940.1131108.1112
162.36560.4482-0.06881.9311-0.10112.02960.00990.0592-0.43560.0066-0.01830.00810.8085-0.17160.01120.6196-0.1372-0.03320.3238-0.03580.329160.709125.7995109.9173
172.68151.52581.49913.24261.10262.22360.0187-0.41350.46920.056-0.25780.6267-0.2917-0.32680.29330.3017-0.00560.06620.3221-0.0320.4258-20.489476.4515119.0811
182.44171.51831.86184.0791.69034.00740.2417-0.1416-0.14550.3594-0.2593-0.17240.4467-0.0955-0.19950.21210.0336-0.01980.29260.06870.3012-7.011363.8797114.7108
193.84020.0537-0.81552.0675-0.56091.9193-0.0041-0.1014-0.3173-0.417-0.2328-0.81870.20281.01850.14950.42560.06470.17640.64280.08160.69439.262563.0775101.5969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 222 through 441 )D222 - 441
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 56 )A1 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 85 )A57 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 119 )A86 - 119
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 188 )A120 - 188
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 221 )A189 - 221
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 246 )A222 - 246
8X-RAY DIFFRACTION8chain 'A' and (resid 247 through 279 )A247 - 279
9X-RAY DIFFRACTION9chain 'A' and (resid 280 through 442 )A280 - 442
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 85 )B1 - 85
11X-RAY DIFFRACTION11chain 'B' and (resid 86 through 188 )B86 - 188
12X-RAY DIFFRACTION12chain 'B' and (resid 189 through 413 )B189 - 413
13X-RAY DIFFRACTION13chain 'B' and (resid 414 through 441 )B414 - 441
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 119 )C1 - 119
15X-RAY DIFFRACTION15chain 'C' and (resid 120 through 246 )C120 - 246
16X-RAY DIFFRACTION16chain 'C' and (resid 247 through 441 )C247 - 441
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 85 )D1 - 85
18X-RAY DIFFRACTION18chain 'D' and (resid 86 through 119 )D86 - 119
19X-RAY DIFFRACTION19chain 'D' and (resid 120 through 221 )D120 - 221

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