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- PDB-6h8b: Molybdenum storage protein prepared under in vivo-like conditions... -

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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 / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Mo5 Cluster / Chem-J7N / Chem-J7Q / molybdate cluster / Chem-J85 / Molybdate cluster / Chem-J8E / MOLYBDATE ION / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
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
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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 (bacteria) / 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 (bacteria) / References: UniProt: P84308

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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

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Experimental details

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Experiment

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

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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

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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

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ndo

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

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)
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 )

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