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- PDB-7ctp: Crystal Structure of Human FAM129B/MINERVA/NIBAN2 -

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Basic information

Entry
Database: PDB / ID: 7ctp
TitleCrystal Structure of Human FAM129B/MINERVA/NIBAN2
ComponentsProtein Niban 2
KeywordsPROTEIN BINDING / PH domain / cytosol / plasma membrane
Function / homology
Function and homology information


gonadotropin secretion / positive regulation of skeletal muscle fiber development / positive regulation of embryonic development / positive regulation of transcription regulatory region DNA binding / positive regulation of gene expression via chromosomal CpG island demethylation / negative regulation of DNA biosynthetic process / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of Notch signaling pathway / axon guidance / negative regulation of angiogenesis ...gonadotropin secretion / positive regulation of skeletal muscle fiber development / positive regulation of embryonic development / positive regulation of transcription regulatory region DNA binding / positive regulation of gene expression via chromosomal CpG island demethylation / negative regulation of DNA biosynthetic process / negative regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of Notch signaling pathway / axon guidance / negative regulation of angiogenesis / adherens junction / cell differentiation / transcription coactivator activity / cadherin binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Niban-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsHahn, H. / Kim, H.S. / Han, B.W.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019R1A2C1090251 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF_2011_0030001 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2020R1C1C1009512 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017R1C1B2012225 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Insight on Functional Regulation of Human MINERVA Protein.
Authors: Hahn, H. / Lee, D.E. / Jang, D.M. / Kim, J. / Lee, Y. / Cheong, H. / Han, B.W. / Kim, H.S.
History
DepositionAug 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Niban 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1374
Polymers64,8601
Non-polymers2763
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-1 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.559, 56.283, 201.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Protein Niban 2 / Meg-3 / Melanoma invasion by ERK / MINERVA / Niban-like protein 1 / Protein FAM129B


Mass: 64860.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NIBAN2, C9orf88, FAM129B / Production host: Escherichia coli (E. coli) / References: UniProt: Q96TA1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.11 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium acetate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jul 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.11 Å / Num. obs: 59778 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.998 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 5794 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→49.11 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 --
Rwork0.2038 --
obs-59470 99.9 %
Displacement parametersBiso mean: 37.41 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 18 269 4806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00594628
X-RAY DIFFRACTIONf_angle_d0.76886240
X-RAY DIFFRACTIONf_chiral_restr0.0462679
X-RAY DIFFRACTIONf_plane_restr0.0047805
X-RAY DIFFRACTIONf_dihedral_angle_d27.75591777
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.3414 259 4.6 %
Rwork0.2943 5547 -
obs--99.2 %

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