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- PDB-4dt2: Crystal structure of red kidney bean purple acid phosphatase in c... -

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Basic information

Entry
Database: PDB / ID: 4dt2
TitleCrystal structure of red kidney bean purple acid phosphatase in complex with Maybridge fragment CC27209
ComponentsPurple acid phosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / phosphatase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region
Similarity search - Function
Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Purple acid phosphatase-like, N-terminal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase, N-terminal / Iron/zinc purple acid phosphatase-like C-terminal domain / Purple acid phosphatase, metallophosphatase domain / Iron/zinc purple acid phosphatase-like protein C / Purple acid Phosphatase, N-terminal domain / Purple acid phosphatase-like, N-terminal / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-0LV / ACETATE ION / : / Fe(3+)-Zn(2+) purple acid phosphatase / Fe(3+)-Zn(2+) purple acid phosphatase
Similarity search - Component
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFeder, D. / Hussein, W.M. / Clayton, D.J. / Kan, M. / Schenk, G. / McGeary, R.P. / Guddat, L.W.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: Identification of purple acid phosphatase inhibitors by fragment-based screening: promising new leads for osteoporosis therapeutics.
Authors: Feder, D. / Hussein, W.M. / Clayton, D.J. / Kan, M.W. / Schenk, G. / McGeary, R.P. / Guddat, L.W.
History
DepositionFeb 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purple acid phosphatase
B: Purple acid phosphatase
C: Purple acid phosphatase
D: Purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,83453
Polymers198,2224
Non-polymers9,61249
Water7,080393
1
A: Purple acid phosphatase
D: Purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,49230
Polymers99,1112
Non-polymers5,38128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-103 kcal/mol
Surface area31770 Å2
MethodPISA
2
B: Purple acid phosphatase
C: Purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,34223
Polymers99,1112
Non-polymers4,23121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-31 kcal/mol
Surface area31880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.760, 126.760, 298.954
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Purple acid phosphatase


Mass: 49555.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaseolus vulgaris (French bean) / Gene: pap
References: UniProt: O24319, UniProt: P80366*PLUS, acid phosphatase

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Sugars , 3 types, 16 molecules

#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#11: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 426 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-0LV / (2,2-dimethyl-2,3-dihydro-1-benzofuran-7-yl)methanol


Mass: 178.228 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14O2
#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.83 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→19.901 Å / Num. obs: 420125

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.72 Å / SU ML: 0.34 / σ(F): 1.23 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 3861 5.02 %
Rwork0.175 --
obs0.178 76897 99.8 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.11 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0854 Å2-0 Å20 Å2
2--0.0854 Å2-0 Å2
3----0.1707 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14040 0 592 393 15025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815133
X-RAY DIFFRACTIONf_angle_d1.14420537
X-RAY DIFFRACTIONf_dihedral_angle_d15.2895493
X-RAY DIFFRACTIONf_chiral_restr0.0782120
X-RAY DIFFRACTIONf_plane_restr0.0052570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.73290.30071280.26612570X-RAY DIFFRACTION100
2.7329-2.76740.31471430.24312592X-RAY DIFFRACTION100
2.7674-2.80380.32031330.23372569X-RAY DIFFRACTION100
2.8038-2.84210.28621140.23372586X-RAY DIFFRACTION100
2.8421-2.88250.31631230.23222625X-RAY DIFFRACTION100
2.8825-2.92540.30981370.22842546X-RAY DIFFRACTION100
2.9254-2.9710.3031440.22412569X-RAY DIFFRACTION100
2.971-3.01950.28511390.21792595X-RAY DIFFRACTION100
3.0195-3.07140.29191460.20422548X-RAY DIFFRACTION100
3.0714-3.12710.25931480.19642538X-RAY DIFFRACTION100
3.1271-3.1870.2551430.19932610X-RAY DIFFRACTION100
3.187-3.25170.26971510.20452626X-RAY DIFFRACTION100
3.2517-3.32210.25641390.18832562X-RAY DIFFRACTION100
3.3221-3.3990.24511310.17542560X-RAY DIFFRACTION100
3.399-3.48360.20861230.15722611X-RAY DIFFRACTION100
3.4836-3.57720.23821270.1642606X-RAY DIFFRACTION100
3.5772-3.68180.23721450.18582601X-RAY DIFFRACTION100
3.6818-3.79980.2071390.15652598X-RAY DIFFRACTION100
3.7998-3.93460.19791320.14292617X-RAY DIFFRACTION100
3.9346-4.09080.19651440.13732627X-RAY DIFFRACTION100
4.0908-4.27520.16911400.12972597X-RAY DIFFRACTION100
4.2752-4.49810.16931470.12972602X-RAY DIFFRACTION100
4.4981-4.77610.16951510.12672625X-RAY DIFFRACTION100
4.7761-5.13880.19621290.1472645X-RAY DIFFRACTION100
5.1388-5.6450.20011490.15932625X-RAY DIFFRACTION100
5.645-6.43680.22431160.17682698X-RAY DIFFRACTION100
6.4368-8.01790.2411630.18652676X-RAY DIFFRACTION100
8.0179-19.71710.22711370.20692812X-RAY DIFFRACTION100

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