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- PDB-4ndr: Crystal structure Molybdenum Storage Protein with fully Mo-loaded... -

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Basic information

Entry
Database: PDB / ID: 4ndr
TitleCrystal structure Molybdenum Storage Protein with fully Mo-loaded cavity
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / Rossmann Fold / Molybdenum Storage / ATP Binding / Molybdenum Binding
Function / homology
Function and homology information


nutrient reservoir activity / molybdenum ion binding / cytoplasm
Similarity search - Function
Molybdenum storage protein subunit alpha/beta / Acetylglutamate kinase-like / Carbamate kinase / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdenum storage protein subunit beta / Chem-8M0 / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / MOLYBDENUM ATOM / Chem-M10 / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPoppe, J. / Warkentin, E. / Demmer, U. / Ermler, U.
CitationJournal: J.Inorg.Biochem. / Year: 2014
Title: Structural diversity of polyoxomolybdate clusters along the three-fold axis of the molybdenum storage protein.
Authors: Poppe, J. / Warkentin, E. / Demmer, U. / Kowalewski, B. / Dierks, T. / Schneider, K. / Ermler, U.
History
DepositionOct 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version

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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)63,73529
Polymers57,7562
Non-polymers5,97927
Water6,449358
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)191,20487
Polymers173,2676
Non-polymers17,93881
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 area35090 Å2
ΔGint-375 kcal/mol
Surface area45960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.270, 114.270, 234.140
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
11A-304-

M10

21A-304-

M10

31B-503-

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


Mass: 28378.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (unknown) / Strain: ATCC 13705 / References: UniProt: P84253
#2: Protein Molybdenum storage protein subunit alpha


Mass: 29376.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (unknown) / Strain: ATCC 13705 / References: UniProt: P84308

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Non-polymers , 7 types, 385 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-8M0 / bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) / Octamolybdate [Mo(VI)8O28]8-


Mass: 1215.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo8O28
#6: Chemical
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mo
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-M10 / (mu3-oxo)-tris(mu2-oxo)-nonakisoxo-trimolybdenum (VI) / Trimolybdate [Mo(VI)3O13]8-


Mass: 495.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo3O13
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0,1 M NaCitrate, 1.1 M (NH4)HCitrate, 0.1 M (NH4)H2PO4, 15% (v/v)EG, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 71122 / Num. obs: 71122 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-2197.8
2-2.1198.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F6T
Resolution: 2→9.996 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 3048 5.03 %Random
Rwork0.1636 ---
all0.1651 60555 --
obs0.1651 60555 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→9.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 164 358 4327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124136
X-RAY DIFFRACTIONf_angle_d1.8395676
X-RAY DIFFRACTIONf_dihedral_angle_d15.2011507
X-RAY DIFFRACTIONf_chiral_restr0.089648
X-RAY DIFFRACTIONf_plane_restr0.007716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0310.32191330.25852565X-RAY DIFFRACTION100
2.031-2.0640.36411420.31762483X-RAY DIFFRACTION96
2.064-2.09930.24361360.22032579X-RAY DIFFRACTION99
2.0993-2.13710.21751370.20392576X-RAY DIFFRACTION100
2.1371-2.17780.2171410.20032589X-RAY DIFFRACTION100
2.1778-2.22170.31851200.29482470X-RAY DIFFRACTION94
2.2217-2.26950.31691220.29632390X-RAY DIFFRACTION92
2.2695-2.32170.19741430.1732615X-RAY DIFFRACTION100
2.3217-2.3790.17931250.15382614X-RAY DIFFRACTION100
2.379-2.44240.19981510.15452601X-RAY DIFFRACTION100
2.4424-2.51310.2271410.16112601X-RAY DIFFRACTION100
2.5131-2.59290.19011350.14462629X-RAY DIFFRACTION100
2.5929-2.68380.19791340.15152611X-RAY DIFFRACTION100
2.6838-2.78910.17821340.14232650X-RAY DIFFRACTION100
2.7891-2.9130.16661330.14272622X-RAY DIFFRACTION100
2.913-3.06240.18121430.14852645X-RAY DIFFRACTION100
3.0624-3.2480.17441390.15132657X-RAY DIFFRACTION100
3.248-3.48890.20731640.13692635X-RAY DIFFRACTION100
3.4889-3.82210.16181380.13382698X-RAY DIFFRACTION100
3.8221-4.33520.14881280.13222692X-RAY DIFFRACTION100
4.3352-5.3210.13691550.14412734X-RAY DIFFRACTION100
5.321-9.9960.1951540.17652851X-RAY DIFFRACTION100
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)
10.6465-0.1604-0.12430.58830.1180.76170.00320.1289-0.057-0.1151-0.00520.08670.0401-0.11420.00870.2578-0.0154-0.020.2109-0.030.217948.07917.381418.6114
24.7592-1.509-1.95554.48692.50152.6897-0.1975-0.2019-0.4610.19450.01730.32110.3806-0.0820.1580.3169-0.0184-0.03610.2409-0.02080.223643.59342.909211.6975
34.3317-4.14660.53025.1614-0.83952.3060.0001-0.0937-0.14920.08630.04540.23710.0285-0.235-0.03850.1399-0.06760.01950.21480.0160.181237.266729.535747.619
40.4984-0.07880.21870.825-0.23091.312-0.0101-0.0248-0.0171-0.00920.0030.07610.0391-0.10190.00270.1394-0.00150.0080.1727-0.00870.1638.21628.385436.9928
57.2055-1.2268-0.36265.0074-0.25353.60220.02820.1941-0.2806-0.38820.08090.82260.3369-0.7972-0.0820.2086-0.0958-0.05980.4268-0.010.357318.878518.334140.1468
64.3849-1.5476-1.54944.99513.29464.0457-0.2278-0.2016-0.38430.38780.16230.27030.4344-0.13530.05440.1743-0.04240.02020.22230.05340.187631.402918.297948.0832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 179 )
2X-RAY DIFFRACTION2chain 'B' and (resid 180 through 270 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 201 )
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 276 )

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