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- PDB-2hpa: STRUCTURAL ORIGINS OF L(+)-TARTRATE INHIBITION OF HUMAN PROSTATIC... -

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Basic information

Entry
Database: PDB / ID: 2hpa
TitleSTRUCTURAL ORIGINS OF L(+)-TARTRATE INHIBITION OF HUMAN PROSTATIC ACID PHOSPHATASE
ComponentsPROTEIN (ACID PHOSPHATASE)
KeywordsHYDROLASE / ACID PHOSPHATASE / N-PROPYLTARTRAMATE
Function / homology
Function and homology information


thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / lysophosphatidic acid phosphatase activity / acid phosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / choline binding / nucleotide metabolic process / vesicle membrane / azurophil granule membrane / dephosphorylation / lysosome organization / phosphatase activity / purine nucleobase metabolic process / multivesicular body / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / filopodium / lipid metabolic process / apical part of cell / molecular adaptor activity / lysosome / lysosomal membrane / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-PROPYL-TARTRAMIC ACID / Prostatic acid phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.9 Å
AuthorsLacount, M.W. / Handy, G. / Lebioda, L.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Structural origins of L(+)-tartrate inhibition of human prostatic acid phosphatase.
Authors: LaCount, M.W. / Handy, G. / Lebioda, L.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Three-Dimensional Structure of Rat Acid Phosphatase in Complex with L(+)-Tartrate
Authors: Lindqvist, Y. / Schneider, G. / Vihko, P.
History
DepositionSep 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 16, 1998Provider: 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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: PROTEIN (ACID PHOSPHATASE)
B: PROTEIN (ACID PHOSPHATASE)
C: PROTEIN (ACID PHOSPHATASE)
D: PROTEIN (ACID PHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,34215
Polymers159,1064
Non-polymers3,23611
Water6,305350
1
A: PROTEIN (ACID PHOSPHATASE)
B: PROTEIN (ACID PHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3488
Polymers79,5532
Non-polymers1,7956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-8 kcal/mol
Surface area28740 Å2
MethodPISA
2
C: PROTEIN (ACID PHOSPHATASE)
D: PROTEIN (ACID PHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9947
Polymers79,5532
Non-polymers1,4415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-3 kcal/mol
Surface area28460 Å2
MethodPISA
3
C: PROTEIN (ACID PHOSPHATASE)
D: PROTEIN (ACID PHOSPHATASE)
hetero molecules

A: PROTEIN (ACID PHOSPHATASE)
B: PROTEIN (ACID PHOSPHATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,34215
Polymers159,1064
Non-polymers3,23611
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-x+3/2,-y+1,z-1/21
Buried area11230 Å2
ΔGint-11 kcal/mol
Surface area56170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.860, 202.680, 71.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.792218, 0.090391, -0.603507), (0.019346, -0.984751, -0.172888), (-0.609932, -0.148641, 0.778389)
Vector: 110.0306, 163.1553, 52.1848)

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PROTEIN (ACID PHOSPHATASE)


Mass: 39776.426 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: ISOLATED FROM HUMAN SEMINAL FLUID / Source: (natural) Homo sapiens (human) / References: UniProt: P15309, acid phosphatase

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Sugars , 4 types, 8 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3/a4-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: 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
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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 , 2 types, 353 molecules

#6: Chemical ChemComp-PT3 / N-PROPYL-TARTRAMIC ACID


Mass: 191.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H13NO5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growpH: 10 / Details: pH 10
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %PEG150011
27 %PEG100011
3100 mM11KCl
4100 mMglycine11

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / 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: 2.9→99 Å / Num. obs: 39548 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 72.3 Å2 / Rmerge(I) obs: 0.138
Reflection
*PLUS
Num. measured all: 224797
Reflection shell
*PLUS
Highest resolution: 2.88 Å / Lowest resolution: 2.98 Å / % possible obs: 60 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.9→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1644 5 %RANDOM
Rwork0.211 ---
obs0.211 32862 88.3 %-
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11204 0 212 350 11766
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.034
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAIN
LS refinement shellResolution: 2.9→3.07 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 216 4.8 %
Rwork0.253 4290 -
obs--73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3TAR.PARTAR.TOP
X-RAY DIFFRACTION4OLIGOSAC.PAROLIGOSAC.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49

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