[English] 日本語
Yorodumi
- PDB-3hmz: CRYSTAL STRUCTURE OF A FMN-BINDING DOMAIN OF FLAVIN REDUCTASES-LI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hmz
TitleCRYSTAL STRUCTURE OF A FMN-BINDING DOMAIN OF FLAVIN REDUCTASES-LIKE ENZYME (SBAL_0626) FROM SHEWANELLA BALTICA OS155 AT 1.50 A RESOLUTION
ComponentsFlavin reductase domain protein, FMN-binding
KeywordsOXIDOREDUCTASE / FMN-BINDING DOMAIN OF FLAVIN REDUCTASES-LIKE ENZYME / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / IMIDAZOLE / Unknown ligand / Flavin reductase domain protein, FMN-binding
Similarity search - Component
Biological speciesShewanella baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of FMN-binding domain of flavin reductases-like enzyme (YP_001049024.1) from Shewanella baltica OS155 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavin reductase domain protein, FMN-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,07110
Polymers22,1731
Non-polymers8989
Water3,945219
1
A: Flavin reductase domain protein, FMN-binding
hetero molecules

A: Flavin reductase domain protein, FMN-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,14320
Polymers44,3472
Non-polymers1,79618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area9240 Å2
ΔGint-11 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.627, 74.627, 74.107
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Flavin reductase domain protein, FMN-binding


Mass: 22173.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella baltica (bacteria) / Strain: OS155 / Gene: Sbal_0626, YP_001049024.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3D092

-
Non-polymers , 5 types, 228 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.22 %
Description: THE STATISTICS REPORTED IN REMARK 200 WERE COMPUTED WITH XSCALE WITH FRIEDEL PAIRS KEPT SEPARATE.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2000M Sodium ThioCyanate, 20.0000% PEG-3350, No Buffer pH 6.9, Additive: 0.0009M flavin-adenine dinucleotide (FAD), VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97797
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97797 Å / Relative weight: 1
ReflectionResolution: 1.5→26.288 Å / Num. obs: 38635 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.061 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.15
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.8531.7255696939199.4
1.55-1.620.5762.4310778307199.8
1.62-1.690.4153.3261596968199.9
1.69-1.780.2714.9280667442199.8
1.78-1.890.1757.5274847250199.9
1.89-2.040.10712286987562199.8
2.04-2.240.06917.9273807207199.8
2.24-2.560.05223.3280317348199.9
2.56-3.230.03332.6283797445199.9
3.23-26.2880.02345.9282887407199.6

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→26.288 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.886 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.052
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ETHYLNE GLYCOL (EDO) AND IMIDAZOLE (IMD) MOLECULES FROM THE CRYOPROTECTION/PURIFICATION SOLUTIONS ARE MODELED. 4. COFACTOR MOLECULE FMN IS MODELED BASED ON THE ELCTRON DENSITY. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED NEAR FMN.
RfactorNum. reflection% reflectionSelection details
Rfree0.15 1933 5 %RANDOM
Rwork0.129 ---
obs0.13 38596 99.87 %-
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 max: 60.49 Å2 / Biso mean: 23.052 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.5→26.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 65 219 1754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221680
X-RAY DIFFRACTIONr_bond_other_d0.0040.021105
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9662305
X-RAY DIFFRACTIONr_angle_other_deg1.39532720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18125.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.915269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.589157
X-RAY DIFFRACTIONr_chiral_restr0.1110.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021904
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02333
X-RAY DIFFRACTIONr_mcbond_it1.94321005
X-RAY DIFFRACTIONr_mcbond_other1.0312403
X-RAY DIFFRACTIONr_mcangle_it2.72631631
X-RAY DIFFRACTIONr_scbond_it2.3472675
X-RAY DIFFRACTIONr_scangle_it3.3223656
X-RAY DIFFRACTIONr_rigid_bond_restr1.46932785
X-RAY DIFFRACTIONr_sphericity_free8.2673229
X-RAY DIFFRACTIONr_sphericity_bonded3.80432735
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 143 -
Rwork0.197 2674 -
all-2817 -
obs--99.58 %

+
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