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- PDB-1hxr: CRYSTAL STRUCTURE OF MSS4 AT 1.65 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1hxr
TitleCRYSTAL STRUCTURE OF MSS4 AT 1.65 ANGSTROMS
ComponentsGUANINE NUCLEOTIDE EXCHANGE FACTOR MSS4
KeywordsMETAL BINDING PROTEIN / nucleotide exchange factor / Rab GTPase / membrane trafficking / Zn binding site
Function / homology
Function and homology information


post-Golgi vesicle-mediated transport / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / protein transport / zinc ion binding / membrane / cytosol
Similarity search - Function
Mss4 / Mss4 protein / MSS4 domain profile. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Guanine nucleotide exchange factor MSS4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SIR/Molecular Replacement / Resolution: 1.65 Å
AuthorsZhu, Z. / Dumas, J.J. / Lietzke, S.E. / Lambright, D.G.
CitationJournal: Biochemistry / Year: 2001
Title: A helical turn motif in Mss4 is a critical determinant of Rab binding and nucleotide release.
Authors: Zhu, Z. / Dumas, J.J. / Lietzke, S.E. / Lambright, D.G.
History
DepositionJan 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 9, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_label_seq_id / _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

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Assembly

Deposited unit
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR MSS4
B: GUANINE NUCLEOTIDE EXCHANGE FACTOR MSS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1304
Polymers26,0002
Non-polymers1312
Water3,369187
1
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR MSS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0652
Polymers13,0001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GUANINE NUCLEOTIDE EXCHANGE FACTOR MSS4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0652
Polymers13,0001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.890, 49.870, 50.680
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GUANINE NUCLEOTIDE EXCHANGE FACTOR MSS4


Mass: 12999.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08326
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG 6000, 50 mM Tris, 50 mM Mg(OAc)2, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 %PEG60001reservoir
250 mMTris-HCl1reservoir
350 mM1reservoirMgOAc2
410 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 24609 / Num. obs: 24609 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.065 / Net I/σ(I): 17.1
Reflection shellResolution: 1.65→7 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1993 / Rsym value: 0.282 / % possible all: 97.2
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.282

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Processing

Software
NameClassification
MLPHAREphasing
X-PLORrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: SIR/Molecular Replacement
Starting model: PDB entry 1FWQ

1fwq


Resolution: 1.65→7 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1132 -Random
Rwork0.214 ---
all-22635 --
obs-22635 96 %-
Refinement stepCycle: LAST / Resolution: 1.65→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 2 187 1865
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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