[English] 日本語
Yorodumi
- PDB-3wjc: Crystal structure of mutant nitrobindin M75L/H76L/Q96C/M148L/H158... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wjc
TitleCrystal structure of mutant nitrobindin M75L/H76L/Q96C/M148L/H158L covalently linked with [Rh(Cp-Mal)(COD)] (NB4-Rh) from Arabidopsis thaliana
ComponentsUPF0678 fatty acid-binding protein-like protein At1g79260
KeywordsTRANSPORT PROTEIN / beta-barrel / intracellular transport / hydrophobic ligands / [Rh(Cp-Mal)(COD)]
Function / homology
Function and homology information


Isomerases; Other isomerases / isomerase activity / metal ion binding / cytosol
Similarity search - Function
Nitrobindin family / THAP4-like, heme-binding beta-barrel domain / THAP4-like, heme-binding beta-barrel domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Chem-RMD / Peroxynitrite isomerase Rv2717c
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMizohata, E. / Fukumoto, K. / Onoda, A. / Bocola, M. / Arlt, M. / Inoue, T. / Schwaneberg, U. / Hayashi, T.
CitationJournal: CHEMCATCHEM / Year: 2014
Title: A Rhodium Complex-linked Hybrid Biocatalyst: Stereo-controlled Phenylacetylene Polymerization within an Engineered Protein Cavity
Authors: Fukumoto, K. / Onoda, A. / Mizohata, E. / Bocola, M. / Inoue, T. / Schwaneberg, U. / Hayashi, T.
History
DepositionOct 8, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0678 fatty acid-binding protein-like protein At1g79260
B: UPF0678 fatty acid-binding protein-like protein At1g79260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2308
Polymers38,8782
Non-polymers1,3526
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-31 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.888, 67.888, 129.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A20 - 160
2113B20 - 160

-
Components

#1: Protein UPF0678 fatty acid-binding protein-like protein At1g79260 / Nitrobindin


Mass: 19439.068 Da / Num. of mol.: 2 / Mutation: M75L, H76L, Q96C, M148L, H158L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g79260, At1g79260.1, YUP8H12R.14 / Plasmid: pET42b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: O64527
#2: Chemical ChemComp-RMD / [(1,2,5,6-eta)-cyclooctane-1,2,5,6-tetrayl]{(1,2,3,4,5-eta)-1-[2-(2,5-dioxopyrrolidin-1-yl)ethyl]cyclopentadienyl}rhodium


Mass: 401.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24NO2Rh
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5mM MES, 200mM NaCl, 100mM MES, 26% polyethylene glycol 400 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11K, H, -L20.5
ReflectionResolution: 2→50 Å / Num. obs: 38003 / % possible obs: 95.9 % / Rsym value: 0.091 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.357 / % possible all: 93

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.874 / SU B: 8.237 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1941 5.1 %RANDOM
Rwork0.23901 ---
obs0.24177 35981 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.307 Å2
Baniso -1Baniso -2Baniso -3
1-6.37 Å20 Å20 Å2
2--6.37 Å20 Å2
3----12.73 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 50 174 2616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.2412.0143378
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1875300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91323.7596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.79615418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9511514
X-RAY DIFFRACTIONr_chiral_restr0.2880.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211848
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9021.51520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7622462
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.063996
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.434.5916
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
560tight positional0.280.05
563loose positional0.425
560tight thermal0.660.5
563loose thermal0.9410
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 139 -
Rwork0.328 2472 -
obs--90.88 %
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)
10.05520.03160.05050.11520.01410.05-0.0104-0.0052-0.01250.00780.0104-0.0062-0.0113-0.0046-0.00010.05830.01230.00460.03870.00380.088528.517-11.4815-13.7169
20.31360.0797-0.02990.19620.05880.0282-0.0031-0.0473-0.05160.0014-0.0068-0.0095-0.00170.00440.010.05580.01670.00420.0630.01130.078911.4544-28.7609-18.1362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 166
2X-RAY DIFFRACTION2B14 - 166

+
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