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- PDB-5uq6: PIG PURPLE ACID PHOSPHATASE COMPLEXED WITH PHOSPHATE IN TWO COORD... -

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Basic information

Entry
Database: PDB / ID: 5uq6
TitlePIG PURPLE ACID PHOSPHATASE COMPLEXED WITH PHOSPHATE IN TWO COORDINATION MODES ALONG WITH A BRIDGING HYDROXIDE ION
ComponentsTartrate-resistant acid phosphatase type 5
KeywordsHYDROLASE / Transition state / metallohydrolase / hydroxide.
Function / homology
Function and homology information


Vitamin B2 (riboflavin) metabolism / acid phosphatase / acid phosphatase activity / bone resorption / ferric iron binding / ferrous iron binding / iron ion transport / extracellular region
Similarity search - Function
Purple acid phosphatase / 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 / Alpha Beta
Similarity search - Domain/homology
: / HYDROXIDE ION / PHOSPHATE ION / Tartrate-resistant acid phosphatase type 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.182 Å
AuthorsSelleck, C. / Guddat, L. / Schenk, G. / Clayton, D.
CitationJournal: Chemistry / Year: 2017
Title: Visualization of the Reaction Trajectory and Transition State in a Hydrolytic Reaction Catalyzed by a Metalloenzyme.
Authors: Selleck, C. / Clayton, D. / Gahan, L.R. / Mitic, N. / McGeary, R.P. / Pedroso, M.M. / Guddat, L.W. / Schenk, G.
History
DepositionFeb 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Tartrate-resistant acid phosphatase type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6227
Polymers35,1541
Non-polymers4686
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-49 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.124, 69.981, 75.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Tartrate-resistant acid phosphatase type 5 / TR-AP / Tartrate-resistant acid ATPase / TrATPase / Type 5 acid phosphatase / Uteroferrin / UF


Mass: 35154.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P09889, 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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 , 5 types, 455 molecules

#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: HO
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% (W/V) PEG3350, 0.1 M LICL, 5% (V/V)ISOPROPANOL, 0.1 M SODIUM CITRATE PH 5.0. PROTEIN CONCENTRATION 38 MG/ML. PROTEIN CONCENTRATION 60MG/ML.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→30.603 Å / Num. obs: 98587 / % possible obs: 91.3 % / Redundancy: 3.957 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.037 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UTE

1ute


Resolution: 1.182→30.603 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.23
RfactorNum. reflection% reflection
Rfree0.1555 1983 2.01 %
Rwork0.1414 --
obs0.1417 98542 90.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.182→30.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 23 450 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072562
X-RAY DIFFRACTIONf_angle_d0.983500
X-RAY DIFFRACTIONf_dihedral_angle_d11.564946
X-RAY DIFFRACTIONf_chiral_restr0.081381
X-RAY DIFFRACTIONf_plane_restr0.008451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1823-1.21190.25511290.26335583X-RAY DIFFRACTION74
1.2119-1.24470.25711420.24576926X-RAY DIFFRACTION92
1.2447-1.28130.28491390.23487043X-RAY DIFFRACTION93
1.2813-1.32270.2221400.21827115X-RAY DIFFRACTION94
1.3227-1.36990.21081410.19997112X-RAY DIFFRACTION94
1.3699-1.42480.19441440.18017107X-RAY DIFFRACTION94
1.4248-1.48960.18131500.15577132X-RAY DIFFRACTION94
1.4896-1.56810.16881440.14147125X-RAY DIFFRACTION94
1.5681-1.66640.14631490.12537111X-RAY DIFFRACTION94
1.6664-1.7950.13551530.12117116X-RAY DIFFRACTION93
1.795-1.97570.13041440.11887067X-RAY DIFFRACTION92
1.9757-2.26150.1361480.11487028X-RAY DIFFRACTION91
2.2615-2.84890.12661370.12066948X-RAY DIFFRACTION90
2.8489-30.61360.14371230.1336146X-RAY DIFFRACTION77
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8124-0.1919-0.0961.84430.25451.16550.00250.05290.0766-0.11960.0128-0.17170.00930.08450.0070.06710.00160.0150.08630.00290.084918.21693.766214.7818
21.3066-0.1076-0.33651.00060.03081.3259-0.0084-0.03040.14380.03740.0477-0.1132-0.02680.1396-0.01550.0871-0.0001-0.01490.1035-0.00860.098917.76429.247727.1109
32.37631.73430.12295.98080.45682.4704-0.0437-0.0890.04840.08250.04310.168-0.0053-0.11790.01820.08080.02890.00220.1107-0.01110.06386.08817.962737.2738
41.0457-0.3609-0.22221.41430.21061.27680.01890.03420.0643-0.0014-0.01730.0395-0.0768-0.14190.01420.08290.01290.0020.09970.00560.08940.812113.273521.337
52.51990.3860.685.01411.62892.77150.0040.07490.3332-0.0971-0.05-0.1526-0.25-0.01220.06440.11260.02080.01480.08820.04230.13519.636621.317712.5386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 147 )
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 175 )
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 271 )
5X-RAY DIFFRACTION5chain 'A' and (resid 272 through 304 )

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