[English] 日本語
Yorodumi
- PDB-2qgi: The UDP complex structure of the sixth gene product of the F1-ATP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qgi
TitleThe UDP complex structure of the sixth gene product of the F1-ATPase operon of Rhodobacter blasticus
ComponentsATP synthase subunits region ORF 6
KeywordsTRANSFERASE / MAJASTRIDIN / ATPASE OPERON / GLYCOSYL TRANSFERASE / ROSSMANN FOLD / UDP-COMPLEX
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta / : / URIDINE-5'-DIPHOSPHATE / ATP synthase subunits region ORF 6
Function and homology information
Biological speciesRhodobacter blasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsEnroth, C. / Strid, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Crystal structure of a protein, structurally related to glycosyltransferases, encoded in the Rhodobacter blasticus atp operon.
Authors: Enroth, C. / Strid, A.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: ATP synthase subunits region ORF 6
B: ATP synthase subunits region ORF 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9555
Polymers57,4412
Non-polymers5143
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-35 kcal/mol
Surface area21120 Å2
MethodPISA
2
A: ATP synthase subunits region ORF 6
B: ATP synthase subunits region ORF 6
hetero molecules

A: ATP synthase subunits region ORF 6
B: ATP synthase subunits region ORF 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,91010
Polymers114,8824
Non-polymers1,0286
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area15230 Å2
ΔGint-88 kcal/mol
Surface area37700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.370, 89.928, 69.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21B-958-

HOH

31B-985-

HOH

DetailsThe assymmetric unit contains one biological unit, i.e. a dimer.

-
Components

#1: Protein ATP synthase subunits region ORF 6


Mass: 28720.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter blasticus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P05449
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM sodium citrate (pH6.0) and 75mM magnesium acetate. Mixed 4+4ul with protein sample, hanging drop, vapor diffusion, temperature 298K., VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 93646 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.071 / Net I/σ(I): 16.7
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 13554 / Rsym value: 0.388 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
SCALACCP4_3.2.17data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NXV

2nxv


Resolution: 1.65→12.99 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.352 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 4687 5 %RANDOM
Rwork0.159 ---
obs0.16 93484 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.201 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→12.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 27 721 4788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0214178
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.9415652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49322.314229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83815667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1311546
X-RAY DIFFRACTIONr_chiral_restr0.2740.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023317
X-RAY DIFFRACTIONr_nbd_refined0.2150.21971
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22834
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2557
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.241
X-RAY DIFFRACTIONr_mcbond_it1.5141.52520
X-RAY DIFFRACTIONr_mcangle_it2.1523922
X-RAY DIFFRACTIONr_scbond_it3.48331897
X-RAY DIFFRACTIONr_scangle_it5.3064.51730
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 361 -
Rwork0.228 6404 -
obs-6765 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)
10.1864-0.0310.10690.27420.01140.2784-0.0006-0.08130.0192-0.0569-0.0246-0.00880.0138-0.00490.0252-0.0064-0.0046-0.012-0.01250.0047-0.022486.4641.58711.173
20.2782-0.0091-0.15760.2697-0.00330.3260.05140.0682-0.02050.0461-0.0763-0.0151-0.0013-0.01710.0249-0.00530.0043-0.0006-0.01570.0057-0.022786.147-5.083-16.558
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2491 - 248
2X-RAY DIFFRACTION2BB2 - 2491 - 248

+
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