[English] 日本語
Yorodumi
- PDB-1qwo: Crystal structure of a phosphorylated phytase from Aspergillus fu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qwo
TitleCrystal structure of a phosphorylated phytase from Aspergillus fumigatus, revealing the structural basis for its heat resilience and catalytic pathway
Componentsphytase
KeywordsHYDROLASE / Alpha Barrel / Beta Sandwich / Orthogonal Bundle / Glycoprotein / phosphohistidine
Function / homology
Function and homology information


3-phytase / 3-phytase activity / acid phosphatase activity / extracellular region
Histidine phosphatase superfamily, clade-2 / Histidine acid phosphatase, eukaryotic / Histidine phosphatase superfamily / Histidine acid phosphatase active site / Histidine phosphatase superfamily (branch 2) / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatases active site signature.
3-phytase A
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsXiang, T. / Liu, Q. / Deacon, A.M. / Koshy, M. / Kriksunov, I.A. / Lei, X.G. / Hao, Q. / Thiel, D.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of a Heat-resilient Phytase from Aspergillus fumigatus, Carrying a Phosphorylated Histidine
Authors: Xiang, T. / Liu, Q. / Deacon, A.M. / Koshy, M. / Kriksunov, I.A. / Lei, X.G. / Hao, Q. / Thiel, D.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: phytase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9457
Polymers48,6171
Non-polymers1,3276
Water11,061614
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)70.340, 70.340, 186.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-954-

HOH

-
Components

#1: Protein/peptide phytase /


Mass: 48617.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Production host: Pichia pastoris (fungus) / References: UniProt: O00092, 3-phytase
#2: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, magnesium chloride hexahydrate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2000
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 69199 / Num. obs: 69199 / % possible obs: 90.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.73 % / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.5→1.53 Å / % possible all: 90.4

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.188 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18561 3529 5.1 %RANDOM
Rwork0.16116 ---
Obs0.16242 65670 91.11 %-
All-69199 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 84 614 4076
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0120.0213552
r_bond_other_d0.0020.023105
r_angle_refined_deg1.4951.9764823
r_angle_other_deg0.90237216
r_dihedral_angle_1_deg6.0055433
r_dihedral_angle_2_deg
r_chiral_restr0.0950.2538
r_gen_planes_refined0.010.023907
r_gen_planes_other0.0130.02727
r_nbd_refined0.2530.2757
r_nbd_other0.250.23705
r_nbtor_other0.0830.21928
r_xyhbond_nbd_refined0.1580.2420
r_xyhbond_nbd_other
r_symmetry_vdw_refined0.280.26
r_symmetry_vdw_other0.3450.238
r_symmetry_hbond_refined0.2090.237
r_symmetry_hbond_other
r_mcbond_it0.791.52163
r_mcangle_it1.4323477
r_scbond_it2.41731389
r_scangle_it3.7354.51346
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 119
Rwork0.243 2420

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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