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- PDB-6hwr: Red kidney bean purple acid phosphatase in complex with adenosine... -

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Basic information

Entry
Database: PDB / ID: 6hwr
TitleRed kidney bean purple acid phosphatase in complex with adenosine divanadate
Components(Fe(3+)-Zn(2+) purple acid ...) x 2
KeywordsMETAL BINDING PROTEIN / Purple acid phosphatase / metallohydrolases / transition state / catalysis / osteoporosis
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / ferric iron binding / extracellular region / zinc ion binding
Similarity search - Function
Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase-like, N-terminal / 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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Purple acid phosphatase-like, N-terminal / Purple acid phosphatase-like / Purple acid phosphatase-like, N-terminal / 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 / 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
: / adenosine divanadate / Chem-H1T / pentakis(oxidanyl)vanadium / ISOPROPYL ALCOHOL / TRIETHYLENE GLYCOL / VANADATE ION / Chem-VV6 / Fe(3+)-Zn(2+) purple acid phosphatase
Similarity search - Component
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFeder, D. / Gahan, L.R. / McGeary, R.P. / Guddat, L.W. / Schenk, G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research CouncilDP150104358 Australia
CitationJournal: Chembiochem / Year: 2019
Title: The Binding Mode of an ADP Analogue to a Metallohydrolase Mimics the Likely Transition State.
Authors: Feder, D. / Gahan, L.R. / McGeary, R.P. / Guddat, L.W. / Schenk, G.
History
DepositionOct 13, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionApr 3, 2019ID: 4KKZ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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 / refine / 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_alt_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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _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_alt_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_alt_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_unobs_or_zero_occ_atoms.label_asym_id / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 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
C: Fe(3+)-Zn(2+) purple acid phosphatase
B: Fe(3+)-Zn(2+) purple acid phosphatase
A: Fe(3+)-Zn(2+) purple acid phosphatase
D: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,46197
Polymers198,2234
Non-polymers12,23993
Water40,1012226
1
C: Fe(3+)-Zn(2+) purple acid phosphatase
D: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,39250
Polymers99,1122
Non-polymers6,28048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12560 Å2
ΔGint-229 kcal/mol
Surface area31320 Å2
MethodPISA
2
B: Fe(3+)-Zn(2+) purple acid phosphatase
A: Fe(3+)-Zn(2+) purple acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,06947
Polymers99,1112
Non-polymers5,95845
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-292 kcal/mol
Surface area31240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.242, 126.242, 296.877
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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Fe(3+)-Zn(2+) purple acid ... , 2 types, 4 molecules CBAD

#1: Protein Fe(3+)-Zn(2+) purple acid phosphatase / PAP / Iron(III)-zinc(II) purple acid phosphatase


Mass: 49555.398 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase
#2: Protein Fe(3+)-Zn(2+) purple acid phosphatase / PAP / Iron(III)-zinc(II) purple acid phosphatase


Mass: 49556.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase

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Sugars , 3 types, 12 molecules

#3: 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.: 3 / Source method: obtained synthetically
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
#4: 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.: 1 / Source method: obtained synthetically
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
#11: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / 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 , 14 types, 2307 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#7: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#12: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#13: Chemical ChemComp-H1T / [[[[bis($l^{1}-oxidanyl)-[$l^{1}-oxidanyl-[tris($l^{1}-oxidanyl)vanadiooxy]vanadio]oxy-vanadio]oxy-bis($l^{1}-oxidanyl)vanadio]oxy-oxidanylidene-vanadio]-[bis($l^{1}-oxidanyl)vanadio]-$l^{3}-oxidanyl]-tetrakis($l^{1}-oxidanyl)vanadium


Mass: 676.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O20V7
#14: Chemical ChemComp-VV6 / [[[[bis(oxidanyl)-[tris(oxidanyl)vanadiooxy]vanadio]oxy-bis(oxidanyl)vanadio]-oxidanylidene-vanadio]oxy-oxidanyl-vanadio]oxy-tetrakis(oxidanyl)vanadium


Mass: 589.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H12O17V6
#15: Chemical ChemComp-H1Q / adenosine divanadate


Mass: 481.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H13N5O11V2
#16: Chemical ChemComp-H1W / pentakis(oxidanyl)vanadium


Mass: 135.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H5O5V
#17: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#18: Chemical ChemComp-VN3 / VANADATE ION / METAVANADATE


Mass: 98.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO3
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2226 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.45 Å3/Da / Density % sol: 64.35 % / Description: Hexagonal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→19.97 Å / Num. obs: 199405 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 19.55 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.07 / Rrim(I) all: 0.226 / Net I/σ(I): 10.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 9 % / Rmerge(I) obs: 1.193 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 28831 / CC1/2: 0.585 / Rpim(I) all: 0.419 / Rrim(I) all: 1.265 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DHL

4dhl


Resolution: 1.95→19.966 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 2001 1 %
Rwork0.1632 --
obs0.1635 199304 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→19.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13988 0 658 2226 16872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715203
X-RAY DIFFRACTIONf_angle_d0.88720735
X-RAY DIFFRACTIONf_dihedral_angle_d17.0275435
X-RAY DIFFRACTIONf_chiral_restr0.0592095
X-RAY DIFFRACTIONf_plane_restr0.0052595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99870.26561420.245613917X-RAY DIFFRACTION100
1.9987-2.05270.27691400.222913941X-RAY DIFFRACTION100
2.0527-2.11310.21351430.20913989X-RAY DIFFRACTION100
2.1131-2.18120.22291420.189513997X-RAY DIFFRACTION100
2.1812-2.2590.24971430.181513981X-RAY DIFFRACTION100
2.259-2.34940.19281410.17114005X-RAY DIFFRACTION100
2.3494-2.45610.22451450.165314000X-RAY DIFFRACTION100
2.4561-2.58530.21761410.163614032X-RAY DIFFRACTION100
2.5853-2.74690.21291410.168214058X-RAY DIFFRACTION100
2.7469-2.95840.20431450.163814114X-RAY DIFFRACTION100
2.9584-3.2550.21671430.157414093X-RAY DIFFRACTION100
3.255-3.72330.16231420.132314206X-RAY DIFFRACTION100
3.7233-4.6810.13591470.121114294X-RAY DIFFRACTION100
4.681-19.96660.19071460.170914676X-RAY DIFFRACTION100

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