[English] 日本語
Yorodumi
- PDB-3fwk: Crystal Structure of Candida glabrata FMN Adenylyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fwk
TitleCrystal Structure of Candida glabrata FMN Adenylyltransferase
ComponentsFMN Adenylyltransferase
KeywordsTRANSFERASE / FAD biosynthesis / alpha/beta protein / Rossmann-like fold / apo-form / extended loop region
Function / homology
Function and homology information


FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / FAD synthase
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsHuerta, C. / Borek, D. / Zhang, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and mechanism of a eukaryotic FMN adenylyltransferase.
Authors: Huerta, C. / Borek, D. / Machius, M. / Grishin, N.V. / Zhang, H.
History
DepositionJan 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FMN Adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2013
Polymers35,9861
Non-polymers2162
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.090, 80.090, 78.089
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein FMN Adenylyltransferase


Mass: 35985.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Strain: NCYC / Gene: CAGL0K01397g, FAD1 / Plasmid: pHIS parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FNA9, FAD synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 6% (w/v) PEG 4000, 0.1 M Sodium acetate, pH 4.6,Temperature 289K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 90728 / Num. obs: 90728 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.07 / Net I/σ(I): 48.224
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.347 / Num. unique all: 4487 / Rsym value: 0.442 / % possible all: 99.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0037refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
RefinementResolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.103 / SU ML: 0.025
Isotropic thermal model: isotropic and anisotropic temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1341 1.5 %RANDOM
Rwork0.162 ---
all0.162 90675 --
obs0.162 90675 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.71 Å2 / Biso mean: 18.769 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 13 390 2905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222586
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9723523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69524.651129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17915466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.61513
X-RAY DIFFRACTIONr_chiral_restr0.1080.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021968
X-RAY DIFFRACTIONr_nbd_refined0.2220.21236
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21794
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.240
X-RAY DIFFRACTIONr_mcbond_it2.61831560
X-RAY DIFFRACTIONr_mcangle_it3.29742473
X-RAY DIFFRACTIONr_scbond_it3.17331189
X-RAY DIFFRACTIONr_scangle_it4.01841044
X-RAY DIFFRACTIONr_rigid_bond_restr1.93432128
X-RAY DIFFRACTIONr_sphericity_free8.148365
X-RAY DIFFRACTIONr_sphericity_bonded6.20731965
LS refinement shellResolution: 1.199→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 104 -
Rwork0.243 6541 -
all-6645 -
obs-6645 99.73 %

+
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://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