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- PDB-2wfq: Crystal structure of the N-terminal signalling domain of human Dh... -

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Basic information

Entry
Database: PDB / ID: 2wfq
TitleCrystal structure of the N-terminal signalling domain of human Dhh without calcium
ComponentsDESERT HEDGEHOG PROTEIN N-PRODUCT
KeywordsSIGNALING PROTEIN / LIPOPROTEIN / DEVELOPMENT / CELL MEMBRANE / AUTOCATALYTIC CLEAVAGE / DISEASE MUTATION / HEDGEHOG SIGNALLING / PROTEASE / MEMBRANE / SECRETED / PALMITATE / HYDROLASE / SIGNAL TRANSDUCTION / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / Ligand-receptor interactions / regulation of steroid biosynthetic process / Transcriptional regulation of testis differentiation / Activation of SMO / patched binding / Leydig cell differentiation / self proteolysis / male sex determination ...cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / Ligand-receptor interactions / regulation of steroid biosynthetic process / Transcriptional regulation of testis differentiation / Activation of SMO / patched binding / Leydig cell differentiation / self proteolysis / male sex determination / Release of Hh-Np from the secreting cell / positive regulation of smoothened signaling pathway / Class B/2 (Secretin family receptors) / cell fate specification / smoothened signaling pathway / spermatid development / protein autoprocessing / myelination / Hedgehog ligand biogenesis / Hedgehog 'on' state / response to estrogen / osteoblast differentiation / cell-cell signaling / response to estradiol / peptidase activity / regulation of gene expression / Hydrolases; Acting on ester bonds / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / extracellular space / zinc ion binding / 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 ...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 / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Desert hedgehog protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBishop, B. / Aricescu, A.R. / Harlos, K. / O'Callaghan, C.A. / Jones, E.Y. / Siebold, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural Insights Into Hedgehog Ligand Sequestration by the Human Hedgehog-Interacting Protein Hip
Authors: Bishop, B. / Aricescu, A.R. / Harlos, K. / O'Callaghan, C.A. / Jones, E.Y. / Siebold, C.
History
DepositionApr 14, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: DESERT HEDGEHOG PROTEIN N-PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0113
Polymers18,8491
Non-polymers1612
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.563, 42.048, 84.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DESERT HEDGEHOG PROTEIN N-PRODUCT / DESERT HEDGEHOG / HHG-3 / DHH


Mass: 18849.082 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SIGNALLING DOMAIN, RESIDUES 39-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O43323
#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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.8 Å3/Da / Density % sol: 35.5 % / Description: NONE
Crystal growDetails: 0.1 M TRIS-HCL, PH 8.5 0.2 M LITHIUM SULFATE 0.2 M SODIUM THIOCYANATE 30% (W/V) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9507
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9507 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 12895 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 12 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0047refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHH

1vhh


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.983 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22895 642 5 %RANDOM
Rwork0.18724 ---
obs0.18918 12205 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.966 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2--2.79 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 6 104 1430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211357
X-RAY DIFFRACTIONr_bond_other_d0.0010.02926
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9351840
X-RAY DIFFRACTIONr_angle_other_deg0.89332223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97222.70374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67615219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.971515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211539
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.5815
X-RAY DIFFRACTIONr_mcbond_other0.1861.5332
X-RAY DIFFRACTIONr_mcangle_it1.16721306
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0863542
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3464.5534
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 50 -
Rwork0.238 876 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -10.816 Å / Origin y: -7.525 Å / Origin z: 10.789 Å
111213212223313233
T0.0293 Å20.0119 Å2-0.0066 Å2-0.0826 Å2-0.0088 Å2--0.0057 Å2
L4.0853 °20.5693 °21.0852 °2-3.1014 °20.7041 °2--3.1898 °2
S0.0986 Å °-0.3474 Å °-0.0633 Å °0.2374 Å °-0.0624 Å °-0.0066 Å °0.0927 Å °-0.1293 Å °-0.0363 Å °

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