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- PDB-1ism: Crystal Structure Analysis of BST-1/CD157 complexed with nicotinamide -

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Basic information

Entry
Database: PDB / ID: 1ism
TitleCrystal Structure Analysis of BST-1/CD157 complexed with nicotinamide
Componentsbone marrow stromal cell antigen 1
KeywordsHYDROLASE / ADP ribosyl cyclase / NAD glycohydrolase / cns / nicotinamide
Function / homology
Function and homology information


: / : / regulation of cellular extravasation / regulation of superoxide metabolic process / regulation of neutrophil chemotaxis / regulation of integrin-mediated signaling pathway / phosphorus-oxygen lyase activity / Post-translational modification: synthesis of GPI-anchored proteins / uropod / Nicotinate metabolism ...: / : / regulation of cellular extravasation / regulation of superoxide metabolic process / regulation of neutrophil chemotaxis / regulation of integrin-mediated signaling pathway / phosphorus-oxygen lyase activity / Post-translational modification: synthesis of GPI-anchored proteins / uropod / Nicotinate metabolism / NAD+ nucleosidase activity / regulation of cell-matrix adhesion / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / humoral immune response / specific granule membrane / side of membrane / positive regulation of B cell proliferation / regulation of peptidyl-tyrosine phosphorylation / regulation of calcium-mediated signaling / regulation of actin cytoskeleton organization / regulation of inflammatory response / transferase activity / positive regulation of cell population proliferation / Neutrophil degranulation / signal transduction / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
ADP Ribosyl Cyclase; Chain A, domain 1 / ADP Ribosyl Cyclase; Chain A, domain 1 / ADP-ribosyl cyclase (CD38/157) / ADP-ribosyl cyclase / NAD(P)-binding Rossmann-like Domain / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYamamoto-Katayama, S. / Ariyoshi, M. / Ishihara, K. / Hirano, T. / Jingami, H. / Morikawa, K.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystallographic studies on human BST-1/CD157 with ADP-ribosyl cyclase and NAD glycohydrolase activities.
Authors: Yamamoto-Katayama, S. / Ariyoshi, M. / Ishihara, K. / Hirano, T. / Jingami, H. / Morikawa, K.
#1: Journal: BIOCHEM.J. / Year: 2001
Title: Site-directed removal of N-glycosylation sites in BST-1/CD157: effects on molecular and functional heterogeneity.
Authors: Yamamoto-Katayama, S. / Sato, A. / Ariyoshi, M. / Suyama, M. / Ishihara, K. / Hirano, T. / Nakamura, H. / Morikawa, K. / Jingami, H.
History
DepositionDec 5, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bone marrow stromal cell antigen 1
B: bone marrow stromal cell antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4376
Polymers60,3442
Non-polymers1,0934
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint10 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.896, 112.728, 133.553
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 bone marrow stromal cell antigen 1 / BST-1/CD157 / ADP-ribosyl cyclase 2


Mass: 30172.182 Da / Num. of mol.: 2 / Fragment: Extracellular region / Mutation: N34D, N63T, N116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q10588, NAD+ glycohydrolase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM

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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: 3.61 Å3/Da / Density % sol: 65.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG4000, citrate, zinc sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 21, 1999 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 16611 / Num. obs: 16611 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 32.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 8
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 32.4 / Num. unique all: 1495 / % possible all: 84.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.97 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 894994.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1223 7.4 %RANDOM
Rwork0.189 ---
all-16589 --
obs-16589 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.3128 Å2 / ksol: 0.355606 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Baniso -1Baniso -2Baniso -3
1-14.59 Å20 Å20 Å2
2---2.89 Å20 Å2
3----11.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 74 0 4084
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it2.871.5
X-RAY DIFFRACTIONc_mcangle_it4.422
X-RAY DIFFRACTIONc_scbond_it4.842
X-RAY DIFFRACTIONc_scangle_it6.812.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 184 7.4 %
Rwork0.295 2318 -
obs-2502 84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3NCA.PARAMNCA.TOP

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