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

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Basic information

Entry
Database: PDB / ID: 2wfr
TitleCrystal structure of the N-terminal signalling domain of human Dhh with 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


regulation of steroid biosynthetic process / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / Ligand-receptor interactions / Transcriptional regulation of testis differentiation / Activation of SMO / patched binding / self proteolysis / Leydig cell differentiation / Release of Hh-Np from the secreting cell ...regulation of steroid biosynthetic process / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / Ligand-receptor interactions / Transcriptional regulation of testis differentiation / Activation of SMO / patched binding / self proteolysis / Leydig cell differentiation / Release of Hh-Np from the secreting cell / male sex determination / positive regulation of smoothened signaling pathway / Class B/2 (Secretin family receptors) / cell fate specification / smoothened signaling pathway / protein autoprocessing / spermatid development / myelination / Hedgehog ligand biogenesis / Hedgehog 'on' state / response to estrogen / osteoblast differentiation / response to estradiol / cell-cell signaling / 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
Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal ...Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / 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: 1.95 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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)19,1876
Polymers18,8491
Non-polymers3385
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.130, 41.880, 83.780
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) / Strain (production host): ROSETTA-GAMI 2(DE3)PLYSS / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.75 Å3/Da / Density % sol: 34.14 % / 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: ESRF / Beamline: ID29 / Wavelength: 0.97623
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 10765 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.6 / % possible all: 91.8

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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 2WFQ

2wfq


Resolution: 1.95→41.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.405 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. RESIDUE Q39 WAS DISORDERED AND MODELED AS AN ALANINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.22487 491 4.6 %RANDOM
Rwork0.17977 ---
obs0.18196 10143 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--1.92 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 13 96 1434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211366
X-RAY DIFFRACTIONr_bond_other_d0.0010.02928
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9381853
X-RAY DIFFRACTIONr_angle_other_deg0.89932228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96422.70374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44215219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6241515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
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_it0.7521.5820
X-RAY DIFFRACTIONr_mcbond_other0.2021.5334
X-RAY DIFFRACTIONr_mcangle_it1.29521313
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1523546
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3644.5540
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 30 -
Rwork0.258 718 -
obs--92.8 %
Refinement TLS params.Method: refined / Origin x: -10.701 Å / Origin y: 7.656 Å / Origin z: -10.808 Å
111213212223313233
T0.0189 Å2-0.0124 Å20.0066 Å2-0.0732 Å2-0.0129 Å2--0.0106 Å2
L3.3738 °2-0.4626 °2-0.7534 °2-3.0751 °20.8039 °2--3.348 °2
S0.046 Å °0.1751 Å °0.125 Å °-0.2182 Å °-0.0138 Å °-0.0246 Å °-0.0793 Å °-0.0766 Å °-0.0322 Å °

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