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- PDB-6vjf: The P-Loop K to A mutation of C. therm Vps1 GTPase-BSE -

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Basic information

Entry
Database: PDB / ID: 6vjf
TitleThe P-Loop K to A mutation of C. therm Vps1 GTPase-BSE
ComponentsPutative sorting protein Vps1
KeywordsHYDROLASE / GTPase / Dynamin / Dynamin Superfamily / BSE / GED / GCP / P-Loop
Function / homology
Function and homology information


GTPase activity / GTP binding / metal ion binding
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Putative sorting protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.472 Å
AuthorsTornabene, B.A. / Varlakhanova, N.V. / Chappie, J.S. / Ford, M.G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120102 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Structural and functional characterization of the dominant negative P-loop lysine mutation in the dynamin superfamily protein Vps1.
Authors: Tornabene, B.A. / Varlakhanova, N.V. / Hosford, C.J. / Chappie, J.S. / Ford, M.G.J.
History
DepositionJan 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative sorting protein Vps1
B: Putative sorting protein Vps1
C: Putative sorting protein Vps1
D: Putative sorting protein Vps1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,95812
Polymers171,7764
Non-polymers2,1828
Water95553
1
A: Putative sorting protein Vps1
B: Putative sorting protein Vps1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9796
Polymers85,8882
Non-polymers1,0914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-34 kcal/mol
Surface area33970 Å2
MethodPISA
2
C: Putative sorting protein Vps1
D: Putative sorting protein Vps1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9796
Polymers85,8882
Non-polymers1,0914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-34 kcal/mol
Surface area33620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.873, 119.032, 84.576
Angle α, β, γ (deg.)90.000, 100.950, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Putative sorting protein Vps1


Mass: 42943.973 Da / Num. of mol.: 4 / Mutation: K58A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061810 / Plasmid: pET-15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: G0SFF0
#2: Chemical
ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 91 mM HEPES pH 8.1 16.7 % PEG 3,350 182 mM Sodium Acetate 3% PROPAN-2-OL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.91299 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 1998
Details: SI 111. ROSENBAUM-ROCK DOUBLE -CRYSTAL MONOCHROMATOR: LIQUID NITROGEN COOLED; SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91299 Å / Relative weight: 1
ReflectionResolution: 2.47→80.38 Å / Num. obs: 56551 / % possible obs: 99.3 % / Redundancy: 7.4 % / Biso Wilson estimate: 55.734 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.024 / Rrim(I) all: 0.067 / Net I/σ(I): 17.3
Reflection shellResolution: 2.47→2.54 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 4608 / CC1/2: 0.954 / Rpim(I) all: 0.157 / Rrim(I) all: 0.445 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
iMOSFLMdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DEF

6def


Resolution: 2.472→80.38 Å / SU ML: 0.202 / Cross valid method: FREE R-VALUE / ESU R: 0.561 / ESU R Free: 0.276
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 2807 5 %RANDOM
Rwork0.1885 ---
obs0.19093 53716 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.2 Å2
Refinement stepCycle: LAST / Resolution: 2.472→80.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11199 0 132 53 11384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015811491
X-RAY DIFFRACTIONf_angle_d1.965615593
X-RAY DIFFRACTIONf_chiral_restr0.10091821
X-RAY DIFFRACTIONf_plane_restr0.00982090
X-RAY DIFFRACTIONf_dihedral_angle_d18.28644498

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