Mass: 8710.016 Da / Num. of mol.: 1 / Fragment: DNA binding Homeobox 2 residues 462-532 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZHX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9UKY1
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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 1H-15N HSQC
1
2
1
2D 1H-13C HSQC
1
3
1
3D HNCO
1
4
1
(4,3)DGFTCABCA(CO)NHN
1
5
1
(4,3)D GFT HNNCABCA
1
6
2
2D 1H-13C HSQC
1
7
1
(4,3)D GFT (H)CCH-COSY alipahtic
1
8
1
3D (H)CCH-TOCSY aliphatic
1
9
1
3D 13C/15N-edited NOESY
1
10
1
(4,3)DGFTHABCAB(CO)NH
1
11
1
3D (H)CCH-COSY aromatic
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.4 mM [U-100% 13C; U-100% 15N] HR7907F, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.3 mM [5% 13C; U-100% 15N] HR7907F, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 1 x Proteinase Inhibitors, 20 mM MES, 50 uM DSS, 90% H2O/10% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.4mM
HR7907F-1
[U-100% 13C; U-100% 15N]
1
0.02 %
sodium azide-2
1
10mM
DTT-3
1
5mM
calcium chloride-4
1
100mM
sodium chloride-5
1
1 %
Proteinase Inhibitors-6
1
20mM
MES-7
1
50uM
DSS-8
1
0.3mM
HR7907F-9
[5% 13C; U-100% 15N]
2
0.02 %
sodium azide-10
2
10mM
DTT-11
2
5mM
calcium chloride-12
2
100mM
sodium chloride-13
2
1 %
Proteinase Inhibitors-14
2
20mM
MES-15
2
50uM
DSS-16
2
Sample conditions
pH: 6.5 / Pressure: 1 atm / Temperature: 298 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
600
1
Varian INOVA
Varian
INOVA
750
2
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Processing
NMR software
Name
Version
Developer
Classification
CARA
1.8.4
KellerandWuthrich
peakpicking
CARA
1.8.4
KellerandWuthrich
chemicalshiftassignment
CYANA
3
Guntert, MumenthalerandWuthrich
refinement
CYANA
3
Guntert, MumenthalerandWuthrich
geometryoptimization
CYANA
3
Guntert, MumenthalerandWuthrich
structuresolution
AS-DP
1
Huang, Tejero, PowersandMontelione
dataanalysis
AS-DP
1
Huang, Tejero, PowersandMontelione
refinement
AutoAssign
2.3.0
Zimmerman, Moseley, KulikowskiandMontelione
dataanalysis
AutoAssign
2.3.0
Zimmerman, Moseley, KulikowskiandMontelione
chemicalshiftassignment
XEASY
Bartelsetal.
dataanalysis
VnmrJ
Varian
collection
TALOS+
Shen, Cornilescu, DelaglioandBax
geometryoptimization
PSVS
Bhattacharya, Montelione
structurevalidation
Refinement
Method: simulated annealing / Software ordinal: 1 Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD NMR ENSEMBLE INFORMATION
NMR constraints
NOE constraints total: 875 / NOE intraresidue total count: 278 / NOE long range total count: 176 / NOE medium range total count: 217 / NOE sequential total count: 204 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 36 / Protein psi angle constraints total count: 36
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20
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