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- PDB-3kbp: KIDNEY BEAN PURPLE ACID PHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 3kbp
TitleKIDNEY BEAN PURPLE ACID PHOSPHATASE
ComponentsPURPLE ACID PHOSPHATASE
KeywordsHYDROLASE (PHOSPHORIC MONOESTER) / PURPLE ACID PHOSPHATASE
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
: / TUNGSTATE(VI)ION / Fe(3+)-Zn(2+) purple acid phosphatase
Similarity search - Component
Biological speciesPhaseolus vulgaris (common bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsKlabunde, T. / Strater, N. / Krebs, B.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures.
Authors: Klabunde, T. / Strater, N. / Frohlich, R. / Witzel, H. / Krebs, B.
#1: Journal: Science / Year: 1995
Title: Crystal Structure of a Purple Acid Phosphatase Containing a Dinuclear Fe(III)-Zn(II) Active Site
Authors: Strater, N. / Klabunde, T. / Tucker, P. / Witzel, H. / Krebs, B.
History
DepositionOct 2, 1995Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)207,11836
Polymers201,2174
Non-polymers5,90132
Water00
1
A: PURPLE ACID PHOSPHATASE
hetero molecules

A: PURPLE ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,55918
Polymers100,6092
Non-polymers2,95016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
2
B: PURPLE ACID PHOSPHATASE
C: PURPLE ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,55918
Polymers100,6092
Non-polymers2,95016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-103 kcal/mol
Surface area30050 Å2
MethodPISA
3
D: PURPLE ACID PHOSPHATASE
hetero molecules

D: PURPLE ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,55918
Polymers100,6092
Non-polymers2,95016
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
4
B: PURPLE ACID PHOSPHATASE
C: PURPLE ACID PHOSPHATASE
hetero molecules

B: PURPLE ACID PHOSPHATASE
C: PURPLE ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,11836
Polymers201,2174
Non-polymers5,90132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area15570 Å2
ΔGint-195 kcal/mol
Surface area57340 Å2
MethodPISA
5
A: PURPLE ACID PHOSPHATASE
D: PURPLE ACID PHOSPHATASE
hetero molecules

A: PURPLE ACID PHOSPHATASE
D: PURPLE ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,11836
Polymers201,2174
Non-polymers5,90132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area15320 Å2
ΔGint-194 kcal/mol
Surface area57740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.700, 347.300, 128.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.149152, -0.169295, -0.974214), (0.000972, -0.985209, 0.171355), (-0.988814, -0.026505, -0.146781)123.3931, 78.4517, 79.2225
2given(-0.143543, 0.177245, 0.973642), (0.002836, -0.983753, 0.179504), (0.98964, 0.028428, 0.140708)9.1121, 77.8473, -14.7662
3given(-0.950461, -0.003169, -0.310828), (0.002421, -0.999993, 0.002794), (-0.310835, 0.001903, 0.950462)139.75861, 178.7711, 21.9883

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Components

#1: Protein
PURPLE ACID PHOSPHATASE


Mass: 50304.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: 111KDA DIMER, COMPLEX WITH TUNGSTATE / Source: (natural) Phaseolus vulgaris (common bean) / References: UniProt: P80366, acid phosphatase
#2: 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.: 20
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
#3: Chemical
ChemComp-FE / FE (III) ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: WO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 64 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlenzyme1drop
24 %PEG100001drop
350 mMsodium acetate1drop
415 %PEG100001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. obs: 50898 / % possible obs: 85.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Num. measured all: 153663
Reflection shell
*PLUS
% possible obs: 79.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 3→10 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.22 -5 %
Rwork0.189 --
obs0.189 40142 69.1 %
Displacement parametersBiso mean: 35.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13976 0 308 0 14284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.559
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.39
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.781
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.39
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.781

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