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- PDB-7f17: Crystal Structure of acid phosphatase -

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Basic information

Entry
Database: PDB / ID: 7f17
TitleCrystal Structure of acid phosphatase
ComponentsAcid phosphatase
KeywordsHYDROLASE / phosphorylation / hydrolysis
Function / homologyAcid phosphatase, class A, bacterial / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / Acid phosphatase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsXu, X. / Hou, X.D. / Song, W. / Rao, Y.J. / Liu, L.M. / Wu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21878126 China
CitationJournal: Acs Catalysis / Year: 2021
Title: Local Electric Field Modulated Reactivity of Pseudomonas aeruginosa Acid Phosphatase for Enhancing Phosphorylation of l-Ascorbic Acid
Authors: Xu, X. / Yan, S. / Hou, X. / Song, W. / Wang, L. / Wu, T. / Qi, M. / Wu, J. / Rao, Y. / Wang, B. / Liu, L.
History
DepositionJun 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid phosphatase
B: Acid phosphatase
C: Acid phosphatase


Theoretical massNumber of molelcules
Total (without water)71,2123
Polymers71,2123
Non-polymers00
Water41423
1
A: Acid phosphatase


Theoretical massNumber of molelcules
Total (without water)23,7371
Polymers23,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acid phosphatase


Theoretical massNumber of molelcules
Total (without water)23,7371
Polymers23,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acid phosphatase


Theoretical massNumber of molelcules
Total (without water)23,7371
Polymers23,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.199, 114.734, 193.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

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Components

#1: Protein Acid phosphatase


Mass: 23737.412 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: phoC, C0044_01345, CAZ10_16160, DT376_10070, DZ962_30070, IPC116_25940, IPC1295_25655, IPC1323_25265, IPC1481_23795, IPC1505_26850, IPC1509_05755, IPC36_01875, IPC582_09790, IPC620_15205, ...Gene: phoC, C0044_01345, CAZ10_16160, DT376_10070, DZ962_30070, IPC116_25940, IPC1295_25655, IPC1323_25265, IPC1481_23795, IPC1505_26850, IPC1509_05755, IPC36_01875, IPC582_09790, IPC620_15205, IPC669_21580, NCTC13621_04764, RW109_RW109_00792
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6FFE3, acid phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 288.5 K / Method: vapor diffusion, sitting drop
Details: 0.1M BIS-TRIS pH 6.5, 50% v/v Polypropylene glycol P 40

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19676 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Χ2: 0.923 / Net I/σ(I): 7.2 / Num. measured all: 248848
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.8511.10.3349340.9690.1030.3510.90598.9
2.85-2.912.80.3499540.9730.1010.3640.913100
2.9-2.9612.90.2919840.9770.0840.3030.89499.8
2.96-3.0213.10.2599730.9860.0740.270.929100
3.02-3.0812.80.2399740.9870.0690.2490.90899.2
3.08-3.1513.10.2129520.9880.0610.220.944100
3.15-3.2312.30.1829860.9890.0530.190.951100
3.23-3.3212.60.1659720.9920.0480.1720.945100
3.32-3.4211.70.1439690.9910.0430.1490.94100
3.42-3.5312.30.1259950.9950.0370.130.992100
3.53-3.6513.30.1129490.9960.0320.1171.012100
3.65-3.813.10.1029790.9950.0290.1071.036100
3.8-3.9713.10.0939930.9950.0270.0971.015100
3.97-4.1813.20.0869810.9970.0240.0890.954100
4.18-4.4412.40.0829980.9970.0240.0850.927100
4.44-4.7912.80.0729860.9990.0210.0760.829100
4.79-5.2713.50.0739940.9980.020.0750.788100
5.27-6.0313.20.07610110.9970.0220.0790.78100
6.03-7.5912.20.06510190.9970.0190.0680.723100
7.59-5011.40.07210730.9980.0230.0761.09399.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→49.37 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 12.379 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 937 4.8 %RANDOM
Rwork0.196 ---
obs0.1982 18611 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.27 Å2 / Biso mean: 41.782 Å2 / Biso min: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å20 Å2
2---0.08 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 2.8→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4887 0 0 23 4910
Biso mean---30 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135033
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174672
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.6526875
X-RAY DIFFRACTIONr_angle_other_deg1.2631.56910828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9035633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3220.659273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.515731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7111545
X-RAY DIFFRACTIONr_chiral_restr0.0720.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
LS refinement shellResolution: 2.8→2.868 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.39 69 -
Rwork0.242 1281 -
obs--96.02 %

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