[English] 日本語
Yorodumi
- PDB-1mrz: Crystal structure of a flavin binding protein from Thermotoga Mar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mrz
TitleCrystal structure of a flavin binding protein from Thermotoga Maritima, TM379
ComponentsRiboflavin kinase/FMN adenylyltransferase
KeywordsTRANSFERASE / Rossmann fold / flavin binding domain / 6-stranded beta barrel / nucleotide binding domain / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


riboflavin metabolic process / riboflavin kinase / FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Riboflavin kinase, bacterial / FAD synthetase / FAD synthetase / Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / HUPs ...Riboflavin kinase, bacterial / FAD synthetase / FAD synthetase / Riboflavin kinase domain, bacterial/eukaryotic / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase / Riboflavin kinase-like / Riboflavin kinase domain superfamily / HUPs / Elongation Factor Tu (Ef-tu); domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Riboflavin biosynthesis protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, W. / Kim, R. / Jancarik, J. / Yokota, H. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2003
Title: Crystal structure of a flavin-binding protein from Thermotoga Maritima
Authors: Wang, W. / Kim, R. / Jancarik, J. / Yokota, H. / Kim, S.-H.
History
DepositionSep 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Riboflavin kinase/FMN adenylyltransferase
B: Riboflavin kinase/FMN adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7164
Polymers67,3322
Non-polymers3842
Water7,963442
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.211, 83.095, 67.851
Angle α, β, γ (deg.)90.00, 116.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Riboflavin kinase/FMN adenylyltransferase / TM379 / Flavin Binding Protein


Mass: 33665.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM379 / Plasmid: pSJS1244 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZW1
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.51 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.2M Na Citrate, 23% PEG 3350, 10% Glycerol, pH 7.5, EVAPORATION, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris1droppH7.5
21 mMEDTA1drop
310 %glycerol1drop
421.5 mg/mlprotein1drop
50.2 mMsodium citrate1reservoir
610 %PEG40001reservoir
75 %glycerol1reservoir
810 %propanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 52473 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rsym value: 0.038 / Net I/σ(I): 27
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 4.1 / Num. unique all: 2670 / Rsym value: 0.299 / % possible all: 82.2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 51627 / Redundancy: 3.8 % / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å / % possible obs: 82.2 % / Redundancy: 3.5 % / Num. unique obs: 2190 / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3

-
Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD

Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.446 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23347 5117 10 %RANDOM
Rwork0.21696 ---
all0.21859 ---
obs0.21696 51065 97.67 %-
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: 21.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20.34 Å2
2--0.91 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 26 442 4814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9765972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5113529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.37215848
X-RAY DIFFRACTIONr_chiral_restr0.0810.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023336
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.32067
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.5555
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.345
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.529
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4481.52649
X-RAY DIFFRACTIONr_mcangle_it0.84124284
X-RAY DIFFRACTIONr_scbond_it1.5631799
X-RAY DIFFRACTIONr_scangle_it2.5244.51688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 392
Rwork0.241 3357
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9394-0.33980.51071.6535-0.34012.4842-0.0502-0.2406-0.1497-0.05250.07430.12280.0896-0.0655-0.02410.0583-0.0113-0.0080.01590.03010.06055.01953.90828.6187
24.9518-2.7412-2.76485.28381.98033.729-0.0757-0.59750.23690.01890.2414-0.61430.00620.7426-0.16570.12150.10850.01120.41830.07580.161633.2126-5.298814.0545
32.8702-0.77860.44321.6285-0.79371.731-0.0762-0.0708-0.06630.09090.15740.0432-0.0954-0.1655-0.08120.077-0.00570.00490.0177-0.00460.056915.2562-9.487651.2756
42.1358-0.3096-0.07134.4312-2.22356.1410.04120.1007-0.2069-0.3040.16090.33040.1802-0.7048-0.20210.10090.0212-0.01010.28720.05980.1185-6.6178-1.404731.5969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1662 - 166
2X-RAY DIFFRACTION2AA178 - 219178 - 219
3X-RAY DIFFRACTION2AA226 - 259226 - 259
4X-RAY DIFFRACTION2AA264 - 288264 - 288
5X-RAY DIFFRACTION3BB302 - 4672 - 167
6X-RAY DIFFRACTION4BB478 - 518178 - 218
7X-RAY DIFFRACTION4BB527 - 589227 - 289
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.12
X-RAY DIFFRACTIONr_improper_angle_d
X-RAY DIFFRACTIONr_improper_angle_deg2.51
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.93 Å

+
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