[English] 日本語
Yorodumi
- PDB-1p9n: Crystal structure of Escherichia coli MobB. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p9n
TitleCrystal structure of Escherichia coli MobB.
ComponentsMolybdopterin-guanine dinucleotide biosynthesis protein B
KeywordsBIOSYNTHETIC PROTEIN / Molybdopterin cofactor biosynthesis / MobB / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / GTP binding / protein homodimerization activity
Similarity search - Function
N-terminal domain of TfIIb - #120 / Molybdopterin-guanine dinucleotide biosynthesis protein B (MobB) domain / Molybdopterin guanine dinucleotide synthesis protein B / N-terminal domain of TfIIb / Single Sheet / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Molybdopterin-guanine dinucleotide biosynthesis adapter protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsRangarajan, S.E. / Tocilj, A. / Li, Y. / Iannuzzi, P. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Molecules of Escherichia coli MobB assemble into densely packed hollow cylinders in a crystal lattice with 75% solvent content.
Authors: Rangarajan, S.E. / Tocilj, A. / Li, Y. / Iannuzzi, P. / Matte, A. / Cygler, M.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Molybdopterin-guanine dinucleotide biosynthesis protein B
B: Molybdopterin-guanine dinucleotide biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4614
Polymers38,2682
Non-polymers1922
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-58 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)239.001, 239.001, 49.046
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Molybdopterin-guanine dinucleotide biosynthesis protein B


Mass: 19134.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MobB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P32125
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.68 M ammonium sulphate, 50 mM Malonic acid, 15 mM cetyl ammonium bromide, 10 mM MgCl2, 1 mM B-mercaptoethanol., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.0 mg/mlprotein1drop
250 mMTris1droppH7.5
3200 mM1dropNaCl
45 mMdithiothreitol1drop
55 %(v/v)glycerol1drop
61.68 Mammonium sulfate1reservoir
70.5 Mmalonic acid1reservoirpH4.5
815 mMacetyl ammonium bromide1reservoir
910 mM1reservoirMgCl2
101 mMbeta-mercaptoethanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97936 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2002 / Details: NULL
RadiationMonochromator: Silicone / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 40361 / Num. obs: 22303 / % possible obs: 86.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.9 Å2 / Rsym value: 0.183
Reflection shellResolution: 2.61→2.7 Å / Rsym value: 0.693 / % possible all: 35.5
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 20053 / % possible obs: 98.5 % / Num. measured all: 241509 / Rmerge(I) obs: 0.183
Reflection shell
*PLUS
% possible obs: 87.5 % / Rmerge(I) obs: 0.716

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→30.92 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1544 9.9 %RANDOM
Rwork0.275 ---
all0.315 20949 --
obs0.275 15664 74.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1812 Å2 / ksol: 0.331851 e/Å3
Displacement parametersBiso mean: 38.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→30.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 10 55 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it5.041.5
X-RAY DIFFRACTIONc_mcangle_it7.532
X-RAY DIFFRACTIONc_scbond_it8.462
X-RAY DIFFRACTIONc_scangle_it9.542.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 126 10.4 %
Rwork0.333 1085 -
obs-1085 35.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 15665 / Num. reflection Rfree: 1545
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

+
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