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- PDB-3n1g: Crystal structure of DhhN bound to BOCFn3 -

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Basic information

Entry
Database: PDB / ID: 3n1g
TitleCrystal structure of DhhN bound to BOCFn3
Components
  • Brother of CDOBOC (gene)
  • Desert hedgehog protein
KeywordsPROTEIN BINDING / Binding Sites / Calcium / Cell Adhesion Molecules / Cell Cycle Proteins / Cell Line / Conserved Sequence / Fibronectins / Hedgehog Proteins / Immunoglobulin G / Membrane Glycoproteins / Membrane Proteins / Tertiary / Receptors / Cell Surface / Sequence Homology / Signal Transduction / Tumor Suppressor Proteins
Function / homology
Function and homology information


cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / regulation of steroid biosynthetic process / Ligand-receptor interactions / 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 / regulation of steroid biosynthetic process / Ligand-receptor interactions / 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 / Myogenesis / protein autoprocessing / spermatid development / positive regulation of myoblast differentiation / axonal growth cone / myelination / Hedgehog ligand biogenesis / axon guidance / Hedgehog 'on' state / cell-cell adhesion / osteoblast differentiation / response to estrogen / cell-cell signaling / response to estradiol / nervous system development / peptidase activity / regulation of gene expression / Hydrolases; Acting on ester bonds / axon / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / extracellular space / zinc ion binding / plasma membrane
Similarity search - Function
Unstructured linking region I-set and fnIII on Brother of CDO / 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 ...Unstructured linking region I-set and fnIII on Brother of CDO / 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 / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Desert hedgehog protein / Brother of CDO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKavran, J.M. / Leahy, D.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: All mammalian Hedgehog proteins interact with cell adhesion molecule, down-regulated by oncogenes (CDO) and brother of CDO (BOC) in a conserved manner.
Authors: Kavran, J.M. / Ward, M.D. / Oladosu, O.O. / Mulepati, S. / Leahy, D.J.
History
DepositionMay 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Desert hedgehog protein
C: Brother of CDO
A: Desert hedgehog protein
D: Brother of CDO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,05411
Polymers63,7394
Non-polymers3157
Water12,791710
1
B: Desert hedgehog protein
C: Brother of CDO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0155
Polymers31,8702
Non-polymers1463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-52 kcal/mol
Surface area12280 Å2
MethodPISA
2
A: Desert hedgehog protein
D: Brother of CDO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0396
Polymers31,8702
Non-polymers1704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-52 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.210, 92.985, 74.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-656-

HOH

21B-667-

HOH

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Components

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Protein , 2 types, 4 molecules BACD

#1: Protein Desert hedgehog protein / / DHH / HHG-3 / Desert hedgehog protein N-product / Desert hedgehog protein C-product


Mass: 19133.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHH / Production host: Escherichia coli (E. coli) / References: UniProt: O43323
#2: Protein Brother of CDO / BOC (gene) / Protein BOC


Mass: 12736.038 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BOC, UNQ604/PRO1190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BWV1

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Non-polymers , 4 types, 717 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 30% PEG 4000, 200 mM MgCl2, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT
DetectorType: RIGAKU SATURN 944+ / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 47802 / Observed criterion σ(F): 1.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→24.648 Å / SU ML: 1.11 / σ(F): 0.01 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 2138 5.09 %
Rwork0.1822 --
obs0.1842 41996 86.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.278 Å2-0 Å2-0 Å2
2---6.9634 Å20 Å2
3----6.4674 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 7 710 4794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074205
X-RAY DIFFRACTIONf_angle_d1.145704
X-RAY DIFFRACTIONf_dihedral_angle_d16.0231544
X-RAY DIFFRACTIONf_chiral_restr0.079592
X-RAY DIFFRACTIONf_plane_restr0.005753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94360.2371940.21131624X-RAY DIFFRACTION54
1.9436-1.99220.27961350.19862432X-RAY DIFFRACTION80
1.9922-2.04610.22211580.17912844X-RAY DIFFRACTION94
2.0461-2.10620.21431630.16632921X-RAY DIFFRACTION97
2.1062-2.17420.20011460.16262950X-RAY DIFFRACTION96
2.1742-2.25180.22281500.16462822X-RAY DIFFRACTION93
2.2518-2.34190.20511480.16972554X-RAY DIFFRACTION84
2.3419-2.44840.24191520.16782488X-RAY DIFFRACTION82
2.4484-2.57740.26361150.17722505X-RAY DIFFRACTION81
2.5774-2.73870.23631120.19162399X-RAY DIFFRACTION78
2.7387-2.94980.22531130.19572391X-RAY DIFFRACTION78
2.9498-3.24610.2481620.17232752X-RAY DIFFRACTION89
3.2461-3.71440.1781620.14723103X-RAY DIFFRACTION100
3.7144-4.67460.17451750.13942937X-RAY DIFFRACTION94
4.6746-24.65050.18421530.16953136X-RAY DIFFRACTION95

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