[English] 日本語
Yorodumi
- PDB-6h8b: Molybdenum storage protein prepared under in vivo-like conditions... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h8b
TitleMolybdenum storage protein prepared under in vivo-like conditions and incubated with ATP and molybdate at 303 K
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / Polyoxometalate clusters / molybdenum storage protein / bionanolab
Function / homology
Function and homology information


nutrient reservoir activity / molybdenum ion binding / cytoplasm
Similarity search - Function
Molybdenum storage protein subunit alpha/beta / Carbamate kinase / Acetylglutamate kinase-like / Amino acid kinase family / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdenum storage protein subunit beta / ADENOSINE-5'-TRIPHOSPHATE / Mo5 Cluster / MOLYBDATE ION / Chem-J8E / Molybdate cluster / Chem-J85 / molybdate cluster / Chem-J7Q / Chem-J7N / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsErmler, U. / Poppe, J.
CitationJournal: J. Inorg. Biochem. / Year: 2018
Title: The molybdenum storage protein - A bionanolab for creating experimentally alterable polyoxomolybdate clusters.
Authors: Brunle, S. / Poppe, J. / Hail, R. / Demmer, U. / Ermler, U.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rsym_value ..._reflns.pdbx_CC_half / _reflns.pdbx_Rsym_value / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rsym_value

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,19512
Polymers57,4932
Non-polymers6,70210
Water3,585199
1
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules

B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,58636
Polymers172,4796
Non-polymers20,10730
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area32320 Å2
ΔGint-212 kcal/mol
Surface area47270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.720, 116.720, 235.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-303-

J8E

21B-303-

J8E

31B-303-

J8E

41B-303-

J8E

51A-305-

J85

61A-305-

J85

71A-305-

J85

81A-305-

J85

91A-306-

MOO

101A-427-

HOH

-
Components

-
Molybdenum storage protein subunit ... , 2 types, 2 molecules BA

#1: Protein Molybdenum storage protein subunit beta / MoSto subunit beta


Mass: 28247.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (unknown) / References: UniProt: P84253
#2: Protein Molybdenum storage protein subunit alpha / Mo storage protein subunit alpha / MoSto subunit alpha


Mass: 29245.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (unknown) / References: UniProt: P84308

-
Non-polymers , 11 types, 209 molecules

#3: Chemical ChemComp-J7T / molybdate cluster


Mass: 1359.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo9O31
#4: Chemical ChemComp-J7N / 2,2,4-tris(oxidanyl)-1,3-dioxa-2$l^{4},4$l^{3}-dimolybdacyclobutane


Mass: 274.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3Mo2O5
#5: Chemical ChemComp-J8E / oxidanyl-[[2,2,4,4,4-pentakis($l^{1}-oxidanyl)-1-(oxidanylmolybdenio)-1$l^{3},3-dioxa-2$l^{5},4$l^{5}-dimolybdacyclobut-2-yl]oxy]molybdenum


Mass: 545.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2Mo4O10
#6: Chemical ChemComp-FUQ / Mo5 Cluster


Mass: 899.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H20Mo5O25
#7: Chemical ChemComp-J7Q / tetrakis($l^{1}-oxidanyl)-[[2,2,2,4,4,4,4,6,6,6,8-undecakis($l^{1}-oxidanyl)-8-(oxidanylmolybdeniooxy)-6-[tris($l^{1}-oxidanyl)molybdeniooxy]-1,3,5,7-tetraoxa-2$l^{6},4$l^{6},6$l^{6},8$l^{4}-tetramolybdacyclooct-2-yl]oxy]molybdenum


Mass: 1088.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMo7O26
#8: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-J8B / Molybdate cluster


Mass: 1183.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo8O26
#11: Chemical ChemComp-J85 / [[[bis(oxidanylmolybdenio)-$l^{3}-oxidanyl]-$l^{1}-oxidanyl-oxidanylidene-molybdenio]-(oxidanylmolybdenio)-$l^{3}-oxidanyl]-tetrakis($l^{1}-oxidanyl)molybdenum


Mass: 658.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3Mo5O11
#12: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 4.03 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium citrate, pH 5.6 1 M NH4H2PO4 10% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 74844 / % possible obs: 99.5 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rsym value: 0.1 / Net I/σ(I): 11.1
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 2 / CC1/2: 0.837 / Rsym value: 0.96

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ndo
Resolution: 1.9→49.415 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.98 / Phase error: 26.52
RfactorNum. reflection% reflection
Rfree0.2468 7061 5.07 %
Rwork0.2336 --
obs0.2343 139264 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 213 197 4219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194151
X-RAY DIFFRACTIONf_angle_d2.9945877
X-RAY DIFFRACTIONf_dihedral_angle_d14.3942415
X-RAY DIFFRACTIONf_chiral_restr0.043630
X-RAY DIFFRACTIONf_plane_restr0.003702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.92170.3892550.38114403X-RAY DIFFRACTION98
1.9217-1.94430.33822080.36934460X-RAY DIFFRACTION98
1.9443-1.9680.36622350.3474394X-RAY DIFFRACTION99
1.968-1.99290.33342670.33174372X-RAY DIFFRACTION99
1.9929-2.01910.33282270.33324475X-RAY DIFFRACTION99
2.0191-2.04680.31522330.32124414X-RAY DIFFRACTION99
2.0468-2.0760.30632550.30614368X-RAY DIFFRACTION99
2.076-2.1070.31112170.30444415X-RAY DIFFRACTION98
2.107-2.13990.30942500.29474426X-RAY DIFFRACTION99
2.1399-2.1750.30832460.29044376X-RAY DIFFRACTION98
2.175-2.21250.28142300.29684381X-RAY DIFFRACTION98
2.2125-2.25280.30692310.28084436X-RAY DIFFRACTION99
2.2528-2.29610.2952690.27534414X-RAY DIFFRACTION99
2.2961-2.34290.26822720.27434401X-RAY DIFFRACTION99
2.3429-2.39390.28092530.26724427X-RAY DIFFRACTION100
2.3939-2.44960.24822350.25934454X-RAY DIFFRACTION99
2.4496-2.51080.27042210.25714441X-RAY DIFFRACTION99
2.5108-2.57870.25562200.24554427X-RAY DIFFRACTION99
2.5787-2.65460.24232080.23064485X-RAY DIFFRACTION99
2.6546-2.74030.24412490.23164374X-RAY DIFFRACTION98
2.7403-2.83820.23042310.21634366X-RAY DIFFRACTION98
2.8382-2.95180.21512290.22234385X-RAY DIFFRACTION98
2.9518-3.08610.25022570.20574411X-RAY DIFFRACTION99
3.0861-3.24880.21492360.19874410X-RAY DIFFRACTION99
3.2488-3.45230.18692320.19334420X-RAY DIFFRACTION99
3.4523-3.71880.23612380.18054365X-RAY DIFFRACTION98
3.7188-4.09290.19742180.17264373X-RAY DIFFRACTION97
4.0929-4.68470.15471880.15414375X-RAY DIFFRACTION96
4.6847-5.90070.18432380.1894358X-RAY DIFFRACTION98
5.9007-49.4320.31432130.28934397X-RAY DIFFRACTION97
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)
17.15990.487-4.7489.0923-2.71148.164-0.01020.37520.5524-0.26860.16890.9008-0.3975-1.4768-0.24190.2089-0.0118-0.09390.5327-0.05710.483321.078629.22124.3173
20.6982-0.03180.07380.4974-0.0360.974-0.06210.1424-0.0849-0.08890.02-0.01120.0805-0.08720.04290.3168-0.00440.00480.2393-0.04290.234754.02515.730917.8248
37.34041.5218-2.4259.14714.37563.7539-0.5298-0.3614-1.04010.57880.1505-0.1111.03060.18490.31460.4913-0.00540.00840.35610.00520.259444.6452-1.51512.48
46.5849-2.6508-4.09052.47632.55454.7599-0.15510.086-0.4889-0.0413-0.07690.15480.4387-0.15250.20760.3966-0.0517-0.03910.2274-0.06710.312843.75585.992911.2335
58.544-3.13462.54161.4252-2.24417.623-0.3541-0.2096-0.86160.27360.18690.36350.60320.03990.190.2501-0.08080.05960.23770.00230.285144.581218.240247.8489
67.2202-5.49535.94726.2869-5.08285.0348-0.1219-0.13690.07340.31180.05750.1213-0.227-0.20410.06130.1665-0.04970.05580.2569-0.01850.233736.394935.767848.5549
71.27610.31881.50010.73911.04654.37120.00710.0724-0.0249-0.10190.00640.0330.0248-0.023-0.00610.1957-0.02280.01920.23280.00630.233941.18230.873933.616
80.2230.0132-0.48042.6373-0.40251.5421-0.08290.1525-0.1177-0.28260.04530.45570.0977-0.47130.03630.2123-0.0314-0.03740.3634-0.05740.24829.839423.619242.141
99.1807-5.3909-0.77657.96222.98784.72510.22310.27550.41030.1048-0.49790.99770.3989-1.34330.15280.2659-0.14280.00450.58210.02890.531119.178717.27743.0657
101.0151-1.01620.09974.19690.83973.5877-0.00380.0329-0.1579-0.0635-0.14730.4390.2054-0.52240.13710.1432-0.06230.02440.3023-0.01890.250130.814520.702544.8352
116.55440.9511-0.29153.35943.41527.75390.0467-0.2273-1.09750.58190.2987-0.19041.29480.1293-0.24670.4299-0.0608-0.03320.3892-0.01020.511530.607214.404851.0349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 28 )
2X-RAY DIFFRACTION2chain 'B' and (resid 29 through 180 )
3X-RAY DIFFRACTION3chain 'B' and (resid 181 through 219 )
4X-RAY DIFFRACTION4chain 'B' and (resid 220 through 270 )
5X-RAY DIFFRACTION5chain 'A' and (resid 32 through 47 )
6X-RAY DIFFRACTION6chain 'A' and (resid 48 through 80 )
7X-RAY DIFFRACTION7chain 'A' and (resid 81 through 169 )
8X-RAY DIFFRACTION8chain 'A' and (resid 170 through 204 )
9X-RAY DIFFRACTION9chain 'A' and (resid 205 through 221 )
10X-RAY DIFFRACTION10chain 'A' and (resid 222 through 261 )
11X-RAY DIFFRACTION11chain 'A' and (resid 262 through 276 )

+
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