[English] 日本語
Yorodumi
- PDB-2d1g: Structure of Francisella tularensis Acid Phosphatase A (AcpA) bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2d1g
TitleStructure of Francisella tularensis Acid Phosphatase A (AcpA) bound to orthovanadate
Componentsacid phosphatase
KeywordsHYDROLASE / Francisella tularensis / Acid Phosphatase / AcpA / decavanadate / vanadate
Function / homology
Function and homology information


phosphoric ester hydrolase activity
Similarity search - Function
Phosphoesterase / Phosphoesterase family / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DECAVANADATE / Chem-ETE / 2-ETHOXYETHANOL / TRIETHYLENE GLYCOL / VANADATE ION / Acid phosphatase / :
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsFelts, R.L. / Reilly, T.J. / Tanner, J.J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of Francisella tularensis AcpA: prototype of a unique superfamily of acid phosphatases and phospholipases C
Authors: Felts, R.L. / Reilly, T.J. / Tanner, J.J.
History
DepositionAug 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: acid phosphatase
B: acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,46411
Polymers112,6782
Non-polymers1,7869
Water9,908550
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-6 kcal/mol
Surface area31800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.081, 144.399, 123.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein acid phosphatase


Mass: 56338.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida (bacteria)
Species: Francisella tularensis / Strain: subsp. novicida / Gene: acpA / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2A5P7, UniProt: A0Q436*PLUS, acid phosphatase

-
Non-polymers , 7 types, 559 molecules

#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#5: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-DVT / DECAVANADATE


Mass: 957.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O28V10
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 1500, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11601
21601
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.127129
SYNCHROTRONAPS 19-ID21.6531
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJul 1, 2004
SBC-32CCDAug 1, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystalSINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1271291
21.65311
ReflectionRedundancy: 14.4 % / Number: 39861 / Rmerge(I) obs: 0.065 / Χ2: 0.985 / D res high: 2.39 Å / D res low: 50 Å / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.392.4810010.1180.93413.4
5.15509910.0561.06713.7
4.095.1510010.0560.87914.4
3.574.0910010.0590.86814.6
3.243.5710010.0661.00114.6
3.013.2410010.0720.91714.6
2.833.0110010.0781.05414.6
2.692.8310010.0861.08114.5
2.572.6910010.0971.08114.5
2.482.5710010.1070.96214.5
ReflectionResolution: 1.75→50 Å / Num. obs: 98137 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.047 / Χ2: 1.015
Reflection shellResolution: 1.75→1.81 Å / % possible obs: 94.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.357 / Num. measured obs: 9497 / Χ2: 0.975

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.75 Å / D res low: 44.23 Å / FOM acentric: 0.364 / FOM centric: 0.489 / Reflection acentric: 92746 / Reflection centric: 5082
Phasing dm shellResolution: 1.75→50 Å / Delta phi final: 0.29 / FOM : 0.315 / Reflection: 98049

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.75→44.28 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.27 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4923 5 %RANDOM
Rwork0.198 ---
all0.2 ---
obs-98094 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---0.91 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.75→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7511 0 90 550 8151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217873
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.94910838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7755959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.98925.602407
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.025151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9241514
X-RAY DIFFRACTIONr_chiral_restr0.0960.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026210
X-RAY DIFFRACTIONr_nbd_refined0.2010.24073
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2682
X-RAY DIFFRACTIONr_metal_ion_refined0.1980.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.218
X-RAY DIFFRACTIONr_mcbond_it0.4991.54846
X-RAY DIFFRACTIONr_mcangle_it0.77727659
X-RAY DIFFRACTIONr_scbond_it1.3933480
X-RAY DIFFRACTIONr_scangle_it1.8854.53115
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 358 -
Rwork0.244 6642 -
all-7000 -
obs--100 %
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)
10.9651-0.3398-0.17480.8885-0.03031.54830.04660.06150.00320.0365-0.0175-0.07130.1820.1939-0.0291-0.20370.0256-0.0402-0.1203-0.0214-0.122643.689438.93965.6175
20.6696-0.2177-0.21592.2039-0.17250.7484-0.0251-0.02690.08120.82050.09920.2248-0.2583-0.0869-0.07410.1870.05580.1165-0.11540.0179-0.099624.083667.520327.1085
39.4024-6.3033-2.99649.7998-2.00775.8684-0.0382-0.03150.02040.36070.20620.5981-0.5267-0.2188-0.168-0.1974-0.01960.0612-0.10670.0232-0.066621.14396.499912.8641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 4895 - 489
2X-RAY DIFFRACTION2BB6 - 4896 - 489
3X-RAY DIFFRACTION3BG2001

+
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