[English] 日本語
Yorodumi
- PDB-2ocx: Crystal structure of Se-Met fucosyltransferase NodZ from Bradyrhi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ocx
TitleCrystal structure of Se-Met fucosyltransferase NodZ from Bradyrhizobium
ComponentsNodulation fucosyltransferase NodZ
KeywordsTRANSFERASE / glycosyltransferase / fucosyltransferase / NodZ / nodulation
Function / homology
Function and homology information


oligosaccharide biosynthetic process / hexosyltransferase activity
Similarity search - Function
Nodulation protein Z / Nodulation protein Z (NodZ) / Glycosyltransferase family 23 (GT23) domain / Glycosyltransferase family 23 (GT23) domain profile. / Rossmann fold - #11340 / Rossmann fold - #11350 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Nodulation fucosyltransferase NodZ
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsBrzezinski, K. / Stepkowski, T. / Panjikar, S. / Bujacz, G. / Jaskolski, M.
Citation
Journal: Acta Biochim.Pol. / Year: 2007
Title: High-resolution structure of NodZ fucosyltransferase involved in the biosynthesis of the nodulation factor.
Authors: Brzezinski, K. / Stepkowski, T. / Panjikar, S. / Bujacz, G. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZ
Authors: Brzezinski, K. / Rogozinski, B. / Stepkowski, T. / Bujacz, G. / Jaskolski, M.
#2: Journal: J.Bacteriol. / Year: 1997
Title: Rhizobium sp. strain NGR234 NodZ protein is a fucosyltransferase
Authors: Quesada-Vincens, D. / Fellay, R. / Nasim, T. / Viprey, V. / Burger, U. / Prome, J.C. / Broughton, W.J. / Jabbouri, S.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Bacterial nodulation protein NodZ is a chitin oligosaccharide fucosyltransferase which can also recognize related substrates of animal origin
Authors: Quinto, C. / Wijfjes, A.H. / Bloemberg, G.V. / Blok-Tip, L. / Lopez-Lara, I.M. / Lugtenberg, B.J. / Thomas-Oates, J.E. / Spaink, H.P.
History
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nodulation fucosyltransferase NodZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5645
Polymers38,1571
Non-polymers4074
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.2, 124.2, 96.2
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

21A-398-

HOH

-
Components

#1: Protein Nodulation fucosyltransferase NodZ


Mass: 38157.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: WM9 / Gene: nodZ / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)RIPL
References: UniProt: Q9AQ17, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3M potassium dihydrogen phosphate, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9537, 0.9787, 0.9790
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2004
RadiationMonochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97871
30.9791
ReflectionResolution: 2.2→20 Å / Num. all: 22641 / Num. obs: 22609 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 42.6 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 56
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 43.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 13.4 / Num. unique all: 2202 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.947 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The refinement included TLS parameters. Residues 179-190, 245-256 and 318-330 were not modeled due to lack of electron density. There was no observed electron density for side chain atoms of ...Details: The refinement included TLS parameters. Residues 179-190, 245-256 and 318-330 were not modeled due to lack of electron density. There was no observed electron density for side chain atoms of residues 87, 102, 118, 119, 177, 178, 191, 193, 227, 258, 259, 305, 306, 307, 310. Those atoms were modeled with zero occupancy and B-factor of 70 A2.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1062 4.7 %RANDOM
Rwork0.184 ---
all0.186 22625 --
obs0.186 22498 99.47 %-
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: 32.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0.71 Å20 Å2
2---1.42 Å20 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 23 180 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222423
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.963290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51122.155116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0071528
X-RAY DIFFRACTIONr_chiral_restr0.090.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022669
X-RAY DIFFRACTIONr_nbd_refined0.2110.2521
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.214
X-RAY DIFFRACTIONr_mcbond_it1.0041.51754
X-RAY DIFFRACTIONr_mcangle_it1.4562.52393
X-RAY DIFFRACTIONr_scbond_it4.06551061
X-RAY DIFFRACTIONr_scangle_it5.57110897
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 84 -
Rwork0.223 1519 -
obs-1603 99.26 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.519-0.2017-0.17073.6049-0.981.58950.0378-0.0868-0.09470.0905-0.0546-0.1882-0.01610.04810.0168-0.17590.00330.0375-0.11480.0092-0.1582-0.396-54.19912.1647
23.6702-2.3207-1.29344.03721.71093.0038-0.0423-0.29310.12580.21430.0714-0.0147-0.06550.1145-0.0292-0.12380.02350.0389-0.08330.0126-0.1169-16.6828-30.64732.6332
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
112 - 1502 - 150
22151 - 317151 - 317

+
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