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- PDB-4djt: Crystal structure of a nuclear GTP-binding protein from Encephali... -

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Basic information

Entry
Database: PDB / ID: 4djt
TitleCrystal structure of a nuclear GTP-binding protein from Encephalitozoon cuniculi bound to GDP-Mg2+
ComponentsGTP-binding nuclear protein GSP1
KeywordsNUCLEAR PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Ran family / GTPase / late sporogonial stage / nucleocytoplasmic transport / RNA export / nuclear transport / fungus
Function / homology
Function and homology information


nucleocytoplasmic transport / protein transport / GTPase activity / GTP binding / nucleus
Similarity search - Function
Ras of Complex, Roc, domain of DAPkinase / Ran GTPase / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding nuclear protein GSP1
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a nuclear GTP-binding protein from Encephalitozoon cuniculi bound to GDP-Mg2+
Authors: Edwards, T.E. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionFeb 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: GTP-binding nuclear protein GSP1
B: GTP-binding nuclear protein GSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2767
Polymers49,3182
Non-polymers9585
Water4,882271
1
A: GTP-binding nuclear protein GSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1273
Polymers24,6591
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding nuclear protein GSP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1504
Polymers24,6591
Non-polymers4903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.570, 89.250, 54.980
Angle α, β, γ (deg.)90.000, 108.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding nuclear protein GSP1 / GTPase Ran homolog


Mass: 24659.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Strain: GB-M1 / Gene: ECU04_1560, GSP1 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SS11
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EncuA.01002.a.A1 PS00532 at 44.6 mg/mL with 5 mM GDP against CSHT screen condition H2: 0.1 M HEPES, pH 7.5, 20% PEG10000, cryoprotectant: 20% ethylene glycol, crystal tracking ID 225457h2, ...Details: EncuA.01002.a.A1 PS00532 at 44.6 mg/mL with 5 mM GDP against CSHT screen condition H2: 0.1 M HEPES, pH 7.5, 20% PEG10000, cryoprotectant: 20% ethylene glycol, crystal tracking ID 225457h2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 13, 2012 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 36266 / Num. obs: 34910 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 27.426 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 34.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.3085.616040237589.1
1.85-1.90.2686.715875236590.7
1.9-1.950.2268.9914528230791.1
1.95-2.010.16710.1916468234395.4
2.01-2.080.13813.914262222093.5
2.08-2.150.11216.2516137226297.9
2.15-2.230.09818.9515599220298.2
2.23-2.320.09322.7114354201393.8
2.32-2.430.07226.3617478202099.1
2.43-2.550.06329.7917782195899.1
2.55-2.680.05834.0617456185698.8
2.68-2.850.04939.2518010175499.3
2.85-3.040.03948.8218628168499.9
3.04-3.290.03261.8619260155299.7
3.29-3.60.0381.1320419141999.7
3.6-4.020.02894.1817816126999.2
4.02-4.650.023100.4816831115099.7
4.65-5.690.024101.361427497099.4
5.69-8.050.02595.051121376299.7
8.050.024111.61578642998.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.1 Å
Translation3 Å45.1 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QG4

1qg4


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.1974 / WRfactor Rwork: 0.1613 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8643 / SU B: 5.206 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1348 / SU Rfree: 0.1278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1740 5 %RANDOM
Rwork0.1752 ---
obs0.1772 34887 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.02 Å2 / Biso mean: 23.4712 Å2 / Biso min: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å2-0.33 Å2
2---0.82 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 59 271 3351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023182
X-RAY DIFFRACTIONr_bond_other_d0.0010.022035
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9624349
X-RAY DIFFRACTIONr_angle_other_deg0.83534971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5725396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7724.552145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0115484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1411512
X-RAY DIFFRACTIONr_chiral_restr0.080.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 110 -
Rwork0.223 2218 -
all-2328 -
obs--88.75 %
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)
10.64080.79120.51061.15430.43710.66-0.0494-0.03540.0519-0.0415-0.02620.0746-0.0674-0.03270.07560.071-0.0019-0.02290.0240.00940.0585.327414.161825.5962
21.8481.3915-0.28492.15570.67330.75550.18250.0638-0.28780.3447-0.144-0.31430.1343-0.1614-0.03850.0778-0.0221-0.03730.03860.01630.076210.26831.736931.9713
30.18260.4820.19151.41740.67970.6531-0.04690.0356-0.0377-0.05350.0671-0.0617-0.03510.0825-0.02030.0624-0.0270.01990.0492-0.0190.05268.49444.718521.3311
411.5415.7235-8.80162.8397-4.36476.71240.02620.1030.02140.03560.0159-0.0015-0.0368-0.0802-0.04220.1052-0.1008-0.09510.10370.10440.116-12.4304-24.104118.5179
50.37960.5589-0.1681.10360.08290.569-0.10520.04210.1125-0.18440.19070.1550.07810.0827-0.08550.071-0.0532-0.04430.08490.0190.04072.2284-13.2261-2.0941
60.48440.1388-0.67370.3233-0.12520.9653-0.0008-0.02260.0630.03930.07140.06630.03040.0513-0.07060.03460.0120.00090.0646-0.01270.04749.1332-10.92290.5305
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 68
2X-RAY DIFFRACTION2A69 - 133
3X-RAY DIFFRACTION3A134 - 195
4X-RAY DIFFRACTION4B-3 - 5
5X-RAY DIFFRACTION5B6 - 122
6X-RAY DIFFRACTION6B123 - 206

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