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- PDB-6a9p: Crystal structure of the human glial fibrillary acidic protein 1B... -

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Basic information

Entry
Database: PDB / ID: 6a9p
TitleCrystal structure of the human glial fibrillary acidic protein 1B domain
ComponentsGlial fibrillary acidic protein
KeywordsSTRUCTURAL PROTEIN / Glial fibrillary acidic protein. GFAP / Intermediate filament / IF / Alexander disease / 1B domain
Function / homology
Function and homology information


regulation of chaperone-mediated autophagy / intermediate filament organization / intermediate filament / intermediate filament cytoskeleton / regulation of protein-containing complex assembly / Nuclear signaling by ERBB4 / structural constituent of cytoskeleton / Chaperone Mediated Autophagy / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glial fibrillary acidic protein / Vasodilator-stimulated phosphoprotein / : / Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. ...Glial fibrillary acidic protein / Vasodilator-stimulated phosphoprotein / : / Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Glial fibrillary acidic protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsJin, M.S. / Kim, B. / Kim, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B4003278 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2018
Title: Crystal structure of the human glial fibrillary acidic protein 1B domain
Authors: Kim, B. / Kim, S. / Jin, M.S.
History
DepositionJul 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Glial fibrillary acidic protein
B: Glial fibrillary acidic protein
C: Glial fibrillary acidic protein
D: Glial fibrillary acidic protein
E: Glial fibrillary acidic protein
F: Glial fibrillary acidic protein
G: Glial fibrillary acidic protein
H: Glial fibrillary acidic protein


Theoretical massNumber of molelcules
Total (without water)100,8328
Polymers100,8328
Non-polymers00
Water2,378132
1
A: Glial fibrillary acidic protein
B: Glial fibrillary acidic protein
G: Glial fibrillary acidic protein
H: Glial fibrillary acidic protein


Theoretical massNumber of molelcules
Total (without water)50,4164
Polymers50,4164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14710 Å2
ΔGint-123 kcal/mol
Surface area26970 Å2
MethodPISA
2
C: Glial fibrillary acidic protein
D: Glial fibrillary acidic protein
E: Glial fibrillary acidic protein
F: Glial fibrillary acidic protein


Theoretical massNumber of molelcules
Total (without water)50,4164
Polymers50,4164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14800 Å2
ΔGint-127 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.588, 106.158, 113.225
Angle α, β, γ (deg.)77.56, 90.14, 83.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glial fibrillary acidic protein / / GFAP


Mass: 12604.056 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFAP / Production host: Escherichia coli (E. coli) / References: UniProt: P14136
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl pH 8.0, 400 mM NaCl and 22% (w/v) PEG10,000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 29465 / % possible obs: 94.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.614

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UF1

3uf1


Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.853 / SU B: 31.932 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31086 1505 4.9 %RANDOM
Rwork0.2686 ---
obs0.27071 29465 84.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.085 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0.88 Å21.74 Å2
2--0.59 Å20.51 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 0 132 6940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196834
X-RAY DIFFRACTIONr_bond_other_d0.0010.026792
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.999180
X-RAY DIFFRACTIONr_angle_other_deg1.725315504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5935812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.30524.413426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.268151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.45815102
X-RAY DIFFRACTIONr_chiral_restr0.0580.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027782
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021548
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.567.663272
X-RAY DIFFRACTIONr_mcbond_other6.55839.6873271
X-RAY DIFFRACTIONr_scbond_it7.2976.1913562
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2668.9385105
X-RAY DIFFRACTIONr_rigid_bond_restr9.92836774
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded65.78256750
LS refinement shellResolution: 2.508→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 44 -
Rwork0.312 796 -
obs--29.98 %

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