[English] 日本語
Yorodumi
- PDB-2i0z: Crystal structure of a FAD binding protein from Bacillus cereus, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i0z
TitleCrystal structure of a FAD binding protein from Bacillus cereus, a putative NAD(FAD)-utilizing dehydrogenases
ComponentsNAD(FAD)-utilizing dehydrogenases
KeywordsOXIDOREDUCTASE / Structural Genomics / NAD(FAD)-utilizing dehydrogenases / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


3-Dehydro-bile acid delta(4,6)-reductase-like / HI0933-like insert domain superfamily / : / HI0933-like protein Rossmann domain / HI0933-like protein barrel and H2TH domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NAD(FAD)-utilizing dehydrogenases
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMinasov, G. / Shuvalova, L. / Vorontsov, I.I. / Kiryukhina, O. / Abdullah, J. / Collart, F.R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a FAD binding protein from Bacillus cereus, a putative NAD(FAD)-utilizing dehydrogenases
Authors: Minasov, G. / Shuvalova, L. / Vorontsov, I.I. / Kiryukhina, O. / Abdullah, J. / Collart, F.R. / Joachimiak, A. / Anderson, W.F.
History
DepositionAug 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(FAD)-utilizing dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8343
Polymers49,0131
Non-polymers8212
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.716, 92.366, 97.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological unit is a monomer

-
Components

#1: Protein NAD(FAD)-utilizing dehydrogenases


Mass: 49012.848 Da / Num. of mol.: 1 / Mutation: P99H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: DSM 31 / Gene: BC_4706 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q816V9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.01M TRIS-HCL, 0.2M Ammonium chloride, 0.25M Sodium chloride, 20% PEG 3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 6, 2006 / Details: mirrors
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.84→25 Å / Num. all: 36967 / Num. obs: 36967 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.9
Reflection shellResolution: 1.84→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3617 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Ice(GM/CA)data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GQF

2gqf


Resolution: 1.84→24.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.237 / SU ML: 0.102
Isotropic thermal model: Isotropic individual atomic B-factors refined
Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24794 1846 5 %RANDOM
Rwork0.19516 ---
obs0.19779 35074 98.87 %-
all-35074 --
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: 34.978 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---2.25 Å20 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.84→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 54 380 3716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223403
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9864617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5985436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96724.718142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47815607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7171518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022532
X-RAY DIFFRACTIONr_nbd_refined0.1990.21678
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22363
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2326
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.223
X-RAY DIFFRACTIONr_mcbond_it1.231.52186
X-RAY DIFFRACTIONr_mcangle_it1.86823422
X-RAY DIFFRACTIONr_scbond_it2.80131402
X-RAY DIFFRACTIONr_scangle_it4.2224.51195
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 129 -
Rwork0.226 2366 -
obs--91.76 %

+
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