[English] 日本語
Yorodumi
- PDB-2gfi: Crystal structure of the phytase from D. castellii at 2.3 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gfi
TitleCrystal structure of the phytase from D. castellii at 2.3 A
Componentsphytase
KeywordsHYDROLASE / 3-phytase
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity
Similarity search - Function
Histidine acid phosphatase, eukaryotic / Histidine acid phosphatases active site signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Phosphoglycerate mutase-like / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDebaryomyces castellii (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHoh, F.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of Debaryomyces castellii CBS 2923 phytase.
Authors: Ragon, M. / Hoh, F. / Aumelas, A. / Chiche, L. / Moulin, G. / Boze, H.
History
DepositionMar 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 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_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 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
Remark 999SEQUENCE No database reference was available at the time of processing.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: phytase
B: phytase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2347
Polymers102,1282
Non-polymers1,1065
Water11,241624
1
A: phytase
B: phytase
hetero molecules

A: phytase
B: phytase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,46814
Polymers204,2564
Non-polymers2,21210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area22350 Å2
ΔGint-50 kcal/mol
Surface area60260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.655, 121.655, 332.245
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a tetramer generated from the dimer by the operation: -y, -x, 1/6-z

-
Components

#1: Protein phytase


Mass: 51063.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Debaryomyces castellii (yeast) / Strain: CBS 2923 / Production host: Debaryomyces castellii (yeast) / References: UniProt: A2TBB4, 3-phytase
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.02M CaCl2 15% MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionRedundancy: 5.1 % / Av σ(I) over netI: 5 / Number: 320802 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / D res high: 2.3 Å / D res low: 65.541 Å / Num. obs: 62779 / % possible obs: 95.2
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
7.2776.7223895.80.0570.0575.4
5.147.27387397.40.0770.0775.9
4.25.144946980.0890.0896
3.644.2580598.20.1010.1016
3.253.64649797.90.1170.1175.9
2.973.25712097.60.1340.1345.9
2.752.97769097.40.160.165.7
2.572.75824597.60.1950.1955.4
2.422.57844094.20.1970.1973.6
2.32.42792584.30.2190.2192.8
ReflectionResolution: 2.29→65.541 Å / Num. obs: 62779 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 5
Reflection shellResolution: 2.29→2.42 Å / % possible obs: 84.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.1 / Num. measured all: 21949 / Num. unique obs: 7925 / Rsym value: 0.219 / % possible all: 83

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QFX

1qfx


Resolution: 2.29→65.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.935 / SU ML: 0.112 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3186 5.1 %RANDOM
Rwork0.154 ---
all0.157 ---
obs-62778 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.29→65.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 70 624 7886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227444
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.94510135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2585914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15325.344378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.537151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9121524
X-RAY DIFFRACTIONr_chiral_restr0.0980.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025812
X-RAY DIFFRACTIONr_nbd_refined0.2180.24422
X-RAY DIFFRACTIONr_nbtor_refined0.320.25359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2873
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.2146
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.246
X-RAY DIFFRACTIONr_mcbond_it1.041.54613
X-RAY DIFFRACTIONr_mcangle_it1.75427347
X-RAY DIFFRACTIONr_scbond_it2.98733179
X-RAY DIFFRACTIONr_scangle_it3.9194.52785
X-RAY DIFFRACTIONr_rigid_bond_restr2.55137792
X-RAY DIFFRACTIONr_sphericity_free6.5953628
X-RAY DIFFRACTIONr_sphericity_bonded2.66137265
LS refinement shellResolution: 2.29→2.346 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 179 -
Rwork0.161 3600 -
obs-3779 79.73 %

+
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://pdbjlvh1.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