[English] 日本語
Yorodumi
- PDB-3ckj: Crystal Structure of a Mycobacterial Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ckj
TitleCrystal Structure of a Mycobacterial Protein
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / mycobacteria
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / glycosyltransferase activity / metal ion binding
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMarland, Z. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of a UDP-glucose-specific glycosyltransferase from a Mycobacterium species.
Authors: Fulton, Z. / McAlister, A. / Wilce, M.C. / Brammananth, R. / Zaker-Tabrizi, L. / Perugini, M.A. / Bottomley, S.P. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T.
History
DepositionMar 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4696
Polymers34,8271
Non-polymers6425
Water1,838102
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,93812
Polymers69,6552
Non-polymers1,28310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7450 Å2
ΔGint-105 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.6, 86.6, 104.3
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Putative uncharacterized protein


Mass: 34827.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium paratuberculosis (bacteria) / Strain: K-10 / References: UniProt: Q73WU1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6 M mono-Ammonium dihydrogen phosphate, 0.1 M Sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9793, 0.9794, 0.9641, 1.0
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97941
30.96411
411
ReflectionResolution: 1.8→100 Å / Num. all: 37229 / Num. obs: 35916 / Redundancy: 4.6 % / Rsym value: 0.03
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.505

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.412 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20124 1158 3.1 %RANDOM
Rwork0.19011 ---
obs0.19046 35916 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 42 102 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222384
X-RAY DIFFRACTIONr_angle_refined_deg1.5682.0073282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5715318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92322.96791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1715362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0891522
X-RAY DIFFRACTIONr_chiral_restr0.1010.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021812
X-RAY DIFFRACTIONr_nbd_refined0.2130.21164
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2146
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.214
X-RAY DIFFRACTIONr_mcbond_it0.9591.51565
X-RAY DIFFRACTIONr_mcangle_it1.41622473
X-RAY DIFFRACTIONr_scbond_it2.363918
X-RAY DIFFRACTIONr_scangle_it3.5814.5800
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 87 -
Rwork0.296 2616 -
obs--100 %
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)
115.05431.9777-2.48552.97043.04224.5971-0.5641-0.3296-0.11741.07630.38480.28510.98731.01520.17940.91490.3623-0.03570.12090.22170.158826.20997.326823.1954
23.0931-1.2890.60824.68520.27084.0177-0.3836-0.5225-0.1761.13780.13760.92680.6617-0.14570.2460.5267-0.02450.32290.15430.10570.14779.630521.824528.4576
32.84760.7334-1.35136.0615-0.72414.0461-0.0422-0.45020.01710.63980.04160.88-0.2176-0.38390.00070.18360.06230.09640.093-0.07550.3096.056937.444520.7474
41.5082-1.1722-0.47254.0881-0.71142.9066-0.2602-0.4616-0.04450.73910.11610.52160.1962-0.22090.14420.24290.02070.09820.0728-0.00050.135512.161629.598123.5026
54.1014-0.4285-1.74974.9046-0.50794.5377-0.3028-0.608-0.38181.03730.16550.29830.77620.26280.13720.64760.13650.09370.16810.12070.195519.079716.563126.1864
61.4323-0.9842-0.66853.07071.31113.5011-0.1261-0.219-0.08140.38750.09720.12360.28380.11630.02890.15510.0118-0.03610.05340.01310.119922.537424.448313.7173
76.34773.2681-0.86687.9402-0.18334.0544-0.2791-0.4128-0.02770.78360.2539-0.04930.49590.57140.02520.39760.1597-0.06040.14430.0330.095425.83720.07120.6647
80.5972-1.76643.79775.2246-11.23324.1511-0.29190.3257-0.70520.82590.01570.73570.9558-0.99560.27620.3724-0.13310.09660.23740.09820.60375.976616.78139.81
93.8072-0.13011.67922.61440.88324.18070.03330.1597-0.0951-0.0709-0.11270.2814-0.0866-0.19460.07940.08650.0083-0.04720.069-0.02530.189813.733528.1154-2.9756
104.3242-0.09950.4996.97073.13199.1271-0.0821-0.51580.28090.7160.07440.0359-0.23380.10290.00770.2620.0025-0.03570.0611-0.07490.23218.494741.290319.3539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 2615 - 26
2X-RAY DIFFRACTION2AA27 - 9827 - 98
3X-RAY DIFFRACTION3AA99 - 12099 - 120
4X-RAY DIFFRACTION4AA121 - 143121 - 143
5X-RAY DIFFRACTION5AA144 - 172144 - 172
6X-RAY DIFFRACTION6AA173 - 244173 - 244
7X-RAY DIFFRACTION7AA245 - 261245 - 261
8X-RAY DIFFRACTION8AA262 - 268262 - 268
9X-RAY DIFFRACTION9AA269 - 315269 - 315
10X-RAY DIFFRACTION10AA316 - 329316 - 329

+
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