- PDB-1qry: Homeobox protein VND (ventral nervous system defective protein) -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1qry
Title
Homeobox protein VND (ventral nervous system defective protein)
Components
PROTEIN (HOMEOBOX VENTRAL NERVOUS SYSTEM DEFECTIVE PROTEIN)
Keywords
DNA BINDING PROTEIN / HELIX-TURN-HELIX / DNA-BINDING PROTEIN
Function / homology
Function and homology information
neuroblast development / neuroblast fate determination / glial cell development / brain development / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II ...neuroblast development / neuroblast fate determination / glial cell development / brain development / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function
STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Representative
Model #1
lowest energy
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Components
#1: Protein
PROTEIN (HOMEOBOXVENTRALNERVOUSSYSTEMDEFECTIVEPROTEIN)
Mass: 9747.162 Da / Num. of mol.: 1 / Fragment: vnd/NK2 homeodomain / Mutation: A35T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)PLYSS / References: UniProt: P22808
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 15N-1H HSQC
1
2
2
3D CBCANH
1
3
2
3DCBCA(CO)NH
1
4
2
3DHBHA(CO)NH
1
5
2
3D HNHA
1
6
3
3D (H)CCH-TOCSY
NMR details
Text: 3D 15N EDITED NOESY-HSQC, 4D 15N/13C EDITED HMQC-NOESY-HSQC, AND 4D 13C/13C EDITED HMQC-NOESY-HSQC WERE USED FOR OBTAINING NOE RESTRAINTS.
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Sample preparation
Details
Solution-ID
Contents
1
0.7 MM A35T VND/NK2-DNA COMPLEX; A35T VND/NK2 IS 15N SINGLE-LABELED; 90% H2O, 10% D2O; PH 6.8
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0.7 MM A35T VND/NK2-DNA COMPLEX; A35T VND/NK2 IS 15N/13C DOUBLE-LABELED; 90% H2O, 10% D2O; PH 6.8
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0.7 MM A35T VND/NK2-DNA COMPLEX; A35T VND/NK2 IS 15N/13C DOUBLE-LABELED; 100% D2O; PH6.8
Sample conditions
pH: 6.8 / Pressure: AMBIENT / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
NMR spectrometer
Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz
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Processing
NMR software
Name
Developer
Classification
NMRPipe
DELAGLIO
processing
X-PLOR
BRUNGER
structuresolution
X-PLOR
BRUNGER
refinement
Refinement
Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON 1146 NOE-DERIVED DISTANCE RESTRAINTS AND 43 DIHEDRAL ANGLE RESTRAINTS.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY Conformers calculated total number: 100 / Conformers submitted total number: 20
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