[English] 日本語
Yorodumi
- PDB-7f17: Crystal Structure of acid phosphatase -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more