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- PDB-9d9v: X-Ray structure of ALX4 homeodomain -

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Basic information

Entry
Database: PDB / ID: 9d9v
TitleX-Ray structure of ALX4 homeodomain
ComponentsHomeobox protein aristaless-like 4
KeywordsTRANSCRIPTION / ALX4 / paired-like homeodomain / transcription factor
Function / homology
Function and homology information


HMG box domain binding / embryonic skeletal system morphogenesis / embryonic forelimb morphogenesis / digestive tract development / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / embryonic digit morphogenesis / muscle organ development / roof of mouth development / hair follicle development ...HMG box domain binding / embryonic skeletal system morphogenesis / embryonic forelimb morphogenesis / digestive tract development / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / embryonic digit morphogenesis / muscle organ development / roof of mouth development / hair follicle development / post-embryonic development / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / nucleus
Similarity search - Function
OAR domain / OAR motif / OAR domain profile. / : / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Homeobox protein aristaless-like 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsYuan, Z. / Kovall, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)1R03TR004875 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM079428 United States
CitationJournal: To Be Published
Title: Structural and biochemical characterization of the ALX4 dimer reveals novel insights into how disease alleles impact ALX4 function
Authors: Yuan, Z. / Kovall, R.A.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeobox protein aristaless-like 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0627
Polymers9,6901
Non-polymers3726
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.780, 95.780, 95.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Homeobox protein aristaless-like 4


Mass: 9689.976 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALX4, KIAA1788 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H161
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.78 Å3/Da / Density % sol: 67.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1M MgCl2, 0.1M KCl, 0.1M PIPES pH=7.0, 20% PEG Smear Medium

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.39→67.73 Å / Num. obs: 5957 / % possible obs: 100 % / Redundancy: 21.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.026 / Rrim(I) all: 0.122 / Χ2: 0.83 / Net I/σ(I): 14.1 / Num. measured all: 130519
Reflection shellResolution: 2.39→2.48 Å / % possible obs: 100 % / Redundancy: 19.8 % / Rmerge(I) obs: 2.81 / Num. measured all: 12377 / Num. unique obs: 626 / CC1/2: 0.495 / Rpim(I) all: 0.646 / Rrim(I) all: 2.884 / Χ2: 0.75 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(dev_4788: ???)refinement
pointlessdata scaling
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→33.86 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 596 10.01 %
Rwork0.2141 --
obs0.2177 5952 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms553 0 24 1 578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008586
X-RAY DIFFRACTIONf_angle_d1.016779
X-RAY DIFFRACTIONf_dihedral_angle_d8.93679
X-RAY DIFFRACTIONf_chiral_restr0.04577
X-RAY DIFFRACTIONf_plane_restr0.01498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.630.37841470.3461326X-RAY DIFFRACTION100
2.63-3.010.37131450.2751322X-RAY DIFFRACTION100
3.01-3.790.28991480.26741337X-RAY DIFFRACTION100
3.8-33.860.19941560.16561371X-RAY DIFFRACTION100

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