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- PDB-5hcn: GPN-loop GTPase Npa3 in complex with GMPPCP -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5hcn
TitleGPN-loop GTPase Npa3 in complex with GMPPCP
ComponentsGPN-loop GTPase 1
KeywordsHYDROLASE / GPN-loop GTPase / Chaperone / Assembly / RNA polymerase
Function / homology
Function and homology information


nucleocytoplasmic transport / mitotic sister chromatid cohesion / protein import into nucleus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol / cytoplasm
Similarity search - Function
GPN-loop GTPase 1 / GPN-loop GTPase / Conserved hypothetical ATP binding protein / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GPN-loop GTPase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNiesser, J. / Wagner, F.R. / Kostrewa, D. / Muehlbacher, W. / Cramer, P.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationGRK1721 Germany
German Research FoundationSFB860 Germany
European Research CouncilTRANSIT Germany
Volkswagen FoundationVW Vorab Germany
CitationJournal: Mol.Cell.Biol. / Year: 2015
Title: Structure of GPN-Loop GTPase Npa3 and Implications for RNA Polymerase II Assembly.
Authors: Niesser, J. / Wagner, F.R. / Kostrewa, D. / Muhlbacher, W. / Cramer, P.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Derived calculations
Revision 1.2Feb 24, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GPN-loop GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5146
Polymers29,5841
Non-polymers9305
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-8 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.240, 116.240, 56.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GPN-loop GTPase 1 / Essential PCL1-interacting ATPase 1 / GPN-loop GTPase NPA3 / Nucleolar preribosomal-associated protein 3


Mass: 29583.822 Da / Num. of mol.: 1 / Fragment: 1-264 delta 203-211 / Mutation: 1-264 delta 203-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NPA3, EPA1, GPN1, YJR072C, J1821 / Production host: Escherichia coli (E. coli)
References: UniProt: P47122, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 281.15 K / Method: small tubes / pH: 7.5
Details: 10 mM HEPES (pH 7.5), 200 mM sodium chloride, 5 mM magnesium chloride, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.99888 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99888 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20172 / % possible obs: 99.5 % / Redundancy: 14.11 % / Rsym value: 0.045 / Net I/σ(I): 28.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 13.12 % / Mean I/σ(I) obs: 2.07 / Rsym value: 1.55 / % possible all: 98

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.758 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 403 2 %
Rwork0.2136 19769 -
obs0.2139 20172 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 242.57 Å2 / Biso mean: 121.3027 Å2 / Biso min: 82.78 Å2
Refinement stepCycle: final / Resolution: 2.2→36.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1998 0 59 5 2062
Biso mean--125 110.68 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072104
X-RAY DIFFRACTIONf_angle_d1.1452836
X-RAY DIFFRACTIONf_chiral_restr0.042315
X-RAY DIFFRACTIONf_plane_restr0.005350
X-RAY DIFFRACTIONf_dihedral_angle_d16.107775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.51840.41251310.32936405653699
2.5184-3.17270.33871330.29165446677100
3.1727-36.76340.18331390.18368206959100
Refinement TLS params.Method: refined / Origin x: 34.9295 Å / Origin y: 18.3738 Å / Origin z: 9.9674 Å
111213212223313233
T1.0421 Å2-0.0097 Å20.0312 Å2-1.0051 Å2-0.0264 Å2--1.0193 Å2
L0.9514 °2-0.5717 °20.169 °2-2.29 °2-1.3507 °2--0.8155 °2
S-0.171 Å °-0.06 Å °-0.2462 Å °0.0813 Å °0.2583 Å °0.2106 Å °-0.1018 Å °-0.0862 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or chain CA2 - 269
2X-RAY DIFFRACTION1chain A or chain CC1

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