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- PDB-3k7j: Crystal structure of the D100E mutant of the Indian Hedgehog N-te... -

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Basic information

Entry
Database: PDB / ID: 3k7j
TitleCrystal structure of the D100E mutant of the Indian Hedgehog N-terminal signalling domain
ComponentsIndian hedgehog protein
KeywordsSIGNALING PROTEIN / alpha+beta sandwich / Autocatalytic cleavage / Cell membrane / Developmental protein / Disease mutation / Glycoprotein / Hydrolase / Lipoprotein / Membrane / Palmitate / Protease / Secreted
Function / homology
Function and homology information


vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / embryonic skeletal joint development / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np ...vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / embryonic skeletal joint development / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / RUNX2 regulates chondrocyte maturation / Ligand-receptor interactions / proteoglycan metabolic process / negative regulation of immature T cell proliferation in thymus / chondrocyte proliferation / negative regulation of T cell differentiation in thymus / retinal pigment epithelium development / positive regulation of T cell differentiation in thymus / epithelial cell-cell adhesion / Activation of SMO / patched binding / embryonic digestive tract morphogenesis / somite development / smooth muscle tissue development / epithelial cell morphogenesis / self proteolysis / head morphogenesis / embryonic pattern specification / Release of Hh-Np from the secreting cell / intein-mediated protein splicing / positive regulation of smoothened signaling pathway / pancreas development / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / regulation of growth / cell fate specification / positive regulation of alpha-beta T cell differentiation / positive regulation of mesenchymal cell proliferation / smoothened signaling pathway / branching involved in blood vessel morphogenesis / embryonic digit morphogenesis / heart looping / protein autoprocessing / positive regulation of collagen biosynthetic process / maternal process involved in female pregnancy / neuron development / response to mechanical stimulus / cell maturation / bone resorption / extracellular matrix / skeletal system development / positive regulation of epithelial cell proliferation / liver regeneration / Hedgehog ligand biogenesis / Hedgehog 'on' state / multicellular organism growth / osteoblast differentiation / cell-cell signaling / response to estradiol / peptidase activity / regulation of gene expression / in utero embryonic development / Hydrolases; Acting on ester bonds / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / plasma membrane
Similarity search - Function
Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Indian hedgehog protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHe, Y.-X. / Kang, Y. / Zhang, W.J. / Yu, J. / Ma, G. / Zhou, C.-Z.
CitationJournal: To be Published
Title: Crystal structure of the D100E mutant of the Indian Hedgehog N-terminal signalling domain
Authors: He, Y.-X. / Kang, Y. / Zhang, W.J. / Yu, J. / Ma, G. / Zhou, C.-Z.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7358
Polymers21,1301
Non-polymers6067
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.160, 52.400, 34.660
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Indian hedgehog protein / / IHH / HHG-2


Mass: 21129.658 Da / Num. of mol.: 1 / Fragment: Indian hedgehog protein N-product / Mutation: D100E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IHH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta / References: UniProt: Q14623
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.81 Å3/Da / Density % sol: 31.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG 4000, 0.2M (NH4)2SO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→24.73 Å / Num. obs: 11849 / % possible obs: 98.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.67 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1680 / % possible all: 97.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHH

1vhh


Resolution: 1.9→18.721 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.808 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 569 4.81 %RANDOM
Rwork0.1999 11264 --
obs0.2035 11833 98.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.547 Å2 / ksol: 0.443 e/Å3
Displacement parametersBiso max: 59.32 Å2 / Biso mean: 26.239 Å2 / Biso min: 14.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.708 Å2-0 Å2-7.897 Å2
2--6.847 Å2-0 Å2
3----4.139 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 30 102 1313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061231
X-RAY DIFFRACTIONf_angle_d0.8861661
X-RAY DIFFRACTIONf_dihedral_angle_d16.786450
X-RAY DIFFRACTIONf_chiral_restr0.064170
X-RAY DIFFRACTIONf_plane_restr0.004211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.0910.27281440.22352761X-RAY DIFFRACTION98
2.091-2.3930.29641480.20062785X-RAY DIFFRACTION99
2.393-3.0130.28511410.20932825X-RAY DIFFRACTION99
3.013-18.7220.24861360.18822893X-RAY DIFFRACTION99

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