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- PDB-1ish: Crystal Structure Analysis of BST-1/CD157 complexed with ethenoNADP -

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Basic information

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


regulation of cellular extravasation / regulation of neutrophil chemotaxis / regulation of superoxide metabolic process / regulation of integrin-mediated signaling pathway / phosphorus-oxygen lyase activity / uropod / Post-translational modification: synthesis of GPI-anchored proteins / Nicotinate metabolism / regulation of cell-matrix adhesion / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase ...regulation of cellular extravasation / regulation of neutrophil chemotaxis / regulation of superoxide metabolic process / regulation of integrin-mediated signaling pathway / phosphorus-oxygen lyase activity / uropod / Post-translational modification: synthesis of GPI-anchored proteins / Nicotinate metabolism / regulation of cell-matrix adhesion / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / humoral immune response / specific granule membrane / side of membrane / positive regulation of B cell proliferation / regulation of calcium-mediated signaling / regulation of actin cytoskeleton organization / transferase activity / regulation of inflammatory response / 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
ETHENO-NADP / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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.occupancy / _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
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)62,5206
Polymers60,3442
Non-polymers2,1754
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint12 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.165, 112.458, 131.302
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-ENP / ETHENO-NADP


Type: RNA linking / Mass: 663.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N5O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: ammonium sulfate, citrate, ethenoNADP, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
162.5 mMNMN11
237.5 mMATP gammaS11
362.5 mMethenoNADP11
462.5 mMethenoNAD11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 16, 2000
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 33495 / Num. obs: 33495 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 30.36 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 3.83
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 17.54 / Num. unique all: 3120 / % possible all: 91.3
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 91.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.46 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1101107.36 / 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
Rfree0.258 2525 7.5 %RANDOM
Rwork0.21 ---
all-33456 --
obs-33456 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.6405 Å2 / ksol: 0.38647 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.81 Å20 Å20 Å2
2---5.58 Å20 Å2
3----9.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 140 202 4352
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_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 380 7.6 %
Rwork0.26 4648 -
obs-5028 88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ETNADPR.PARAMETNADPR.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_d1.205
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.305 / % reflection Rfree: 7.6 % / Rfactor Rwork: 0.26

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