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- PDB-4kzg: Crystal structure of zebrafish MO25 -

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Basic information

Entry
Database: PDB / ID: 4kzg
TitleCrystal structure of zebrafish MO25
ComponentsZgc:86716
KeywordsSIGNALING PROTEIN / Scaffold protein / Kinase activator / STE20 kinases
Function / homology
Function and homology information


protein kinase activator activity / protein serine/threonine kinase activator activity / intracellular signal transduction
Similarity search - Function
Mo25-like / Mo25-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, Z.Z. / Shi, Z.B. / Zhang, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of zebrafish MO25
Authors: Zhang, Z.Z. / Wang, Y.C. / Shi, Z.B. / Zhang, M.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zgc:86716
B: Zgc:86716
C: Zgc:86716
D: Zgc:86716
E: Zgc:86716
F: Zgc:86716
G: Zgc:86716
H: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)304,8318
Polymers304,8318
Non-polymers00
Water70339
1
A: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)38,1041
Polymers38,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)38,1041
Polymers38,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)38,1041
Polymers38,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)38,1041
Polymers38,1041
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)38,1041
Polymers38,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)38,1041
Polymers38,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)38,1041
Polymers38,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Zgc:86716


Theoretical massNumber of molelcules
Total (without water)38,1041
Polymers38,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.665, 156.665, 221.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments: (Selection details: chain 'H' RESTRAINED TORSIONS: 12159 Histogram of differences under limit:...)

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Components

#1: Protein
Zgc:86716 / MO25


Mass: 38103.844 Da / Num. of mol.: 8 / Fragment: UNP residues residues 12-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cab39 / Plasmid: HT-pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codonplus / References: UniProt: Q6IQL2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Lithium citrate tribasic tetrahydrate, 20% w/v Polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 70189 / Num. obs: 70049 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 34.69 Å2 / Rmerge(I) obs: 0.172
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.86 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UPL

1upl


Resolution: 2.9→49.956 Å / Occupancy max: 1 / Occupancy min: 0.27 / SU ML: 0.39 / σ(F): 1.33 / Phase error: 39.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3266 1975 2.85 %
Rwork0.2878 --
obs0.2889 69358 98.68 %
all-70280 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.04 Å2 / Biso mean: 23.9724 Å2 / Biso min: 3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20024 0 0 39 20063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320365
X-RAY DIFFRACTIONf_angle_d0.88127477
X-RAY DIFFRACTIONf_dihedral_angle_d12.9077560
X-RAY DIFFRACTIONf_chiral_restr0.0353183
X-RAY DIFFRACTIONf_plane_restr0.0033511
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11HX-RAY DIFFRACTIONPOSITIONAL
12HX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8972-2.96970.36851310.31284645477697
2.9697-3.050.38681370.32334797493499
3.05-3.13970.35621410.33824769491099
3.1397-3.2410.32651440.31384823496799
3.241-3.35680.37271430.29834767491099
3.3568-3.49120.40531410.29324794493599
3.4912-3.650.32631390.29044849498899
3.65-3.84240.3261420.27764767490999
3.8424-4.0830.27791400.27164790493099
4.083-4.39810.29551400.26044824496499
4.3981-4.84040.29511410.24384840498199
4.8404-5.540.30841420.26174851499399
5.54-6.97680.34271480.29914922507099
6.9768-49.96380.30241460.30994945509196
Refinement TLS params.Method: refined / Origin x: 34.0166 Å / Origin y: 36.0955 Å / Origin z: 50.6429 Å
111213212223313233
T-0.0454 Å2-0.0213 Å2-0.0341 Å2-0.1044 Å2-0.0379 Å2--0.0698 Å2
L0.0347 °20.032 °2-0.0551 °2-0.0886 °20.0454 °2--0.0553 °2
S-0.0043 Å °0.0797 Å °-0.0137 Å °0.1098 Å °0.0222 Å °0.0043 Å °-0.0017 Å °0.0396 Å °0.001 Å °
Refinement TLS groupSelection details: all

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