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- PDB-5ub8: Crystal structure of YPT31, a Rab family GTPase from Candida albi... -

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Basic information

Entry
Database: PDB / ID: 5ub8
TitleCrystal structure of YPT31, a Rab family GTPase from Candida albicans, in complex with GDP and Zn(II)
ComponentsLikely rab family GTP-binding protein
KeywordsPROTEIN BINDING / G-PROTEIN / RAB / GDP / P-LOOP / GTPASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID
Function / homology
Function and homology information


cellular response to xenobiotic stimulus => GO:0071466 / exocytosis / recycling endosome / endosome / GTPase activity / GTP binding / metal ion binding
Similarity search - Function
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 / Rab family GTPase / :
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsStogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSCN27220120026C United States
CitationJournal: To Be Published
Title: Crystal structure of YPT31, a Rab family GTPase from Candida albicans, in complex with GDP and Zn(II)
Authors: Stogios, P.J.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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_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.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_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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Likely rab family GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6234
Polymers25,0491
Non-polymers5743
Water2,288127
1
A: Likely rab family GTP-binding protein
hetero molecules

A: Likely rab family GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2468
Polymers50,0982
Non-polymers1,1486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4050 Å2
ΔGint-150 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.303, 43.392, 41.662
Angle α, β, γ (deg.)90.00, 89.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

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Components

#1: Protein Likely rab family GTP-binding protein


Mass: 25048.908 Da / Num. of mol.: 1
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: YPT31, CaO19.10153, CaO19.2622, orf19.2622 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: Q59KX4, UniProt: A0A1D8PTI2*PLUS
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15% (w/v) PEG3350, 25 mM zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 8864 / % possible obs: 98.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 13.13
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 2.56 / CC1/2: 0.605 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CPJ

3cpj


Resolution: 2.35→29.572 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.9
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 836 10.02 %RANDOM
Rwork0.1853 ---
obs0.1893 8343 92.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 30 127 1562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021466
X-RAY DIFFRACTIONf_angle_d0.5861985
X-RAY DIFFRACTIONf_dihedral_angle_d22.81539
X-RAY DIFFRACTIONf_chiral_restr0.043219
X-RAY DIFFRACTIONf_plane_restr0.002248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3459-2.49280.26711250.25331112X-RAY DIFFRACTION83
2.4928-2.68510.29141300.23661165X-RAY DIFFRACTION87
2.6851-2.95510.29541440.22931231X-RAY DIFFRACTION92
2.9551-3.38220.25321360.19381292X-RAY DIFFRACTION95
3.3822-4.25920.20061470.15791330X-RAY DIFFRACTION98
4.2592-29.5740.1671540.15161377X-RAY DIFFRACTION99
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)
13.83732.52051.40542.47540.40142.7328-0.02650.1571-0.3756-0.08940.228-0.33670.20010.5708-0.19330.23130.0840.00220.24370.03060.268449.576829.933610.5986
26.74123.7068-0.92924.8528-0.31542.56610.0845-0.1268-0.46210.0171-0.0206-0.44980.13240.4134-0.060.18110.0337-0.04820.21770.00910.185145.973828.021316.4269
33.2765-1.9642.47931.323-1.06055.247-0.0915-0.0173-0.23170.137-0.05410.03080.1045-0.17040.11310.2117-0.04770.0510.13640.01310.205830.742732.992414.6115
42.6896-0.2406-3.67237.80433.07065.91480.15630.12920.3135-0.11170.2233-0.3736-0.35070.5504-0.22110.12070.0405-0.00280.10210.06170.234138.168135.649510.0733
52.20460.19051.39272.23770.30322.5177-0.00610.12750.1969-0.0498-0.0655-0.2646-0.10610.48610.05540.1534-0.00530.0480.20630.05370.153639.882839.83116.7058
64.70514.9584-1.36715.2309-1.51322.0325-0.5222-1.30910.10131.4074-0.45350.33022.23610.61350.98441.28450.1760.04340.6055-0.10080.596352.562351.899423.6092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:42)
2X-RAY DIFFRACTION2(chain A and resid 43:92)
3X-RAY DIFFRACTION3(chain A and resid 93:116)
4X-RAY DIFFRACTION4(chain A and resid 117:133)
5X-RAY DIFFRACTION5(chain A and resid 134:181)
6X-RAY DIFFRACTION6(chain A and resid 182:186)

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