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

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Basic information

Entry
Database: PDB / ID: 4ndo
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 / 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
Chem-8M0 / ADENOSINE-5'-TRIPHOSPHATE / Chem-M10 / MOLYBDENUM ATOM / PHOSPHATE 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: 1.35 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
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)63,83130
Polymers57,7562
Non-polymers6,07528
Water8,557475
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)191,49290
Polymers173,2676
Non-polymers18,22684
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 area35450 Å2
ΔGint-406 kcal/mol
Surface area47210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.600, 115.600, 234.100
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-313-

MO

21B-314-

MO

31A-304-

M10

41A-304-

M10

51A-309-

MO

61B-517-

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 / Mo storage protein subunit beta / MoSto subunit beta


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


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

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Non-polymers , 7 types, 503 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-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
#5: Chemical...
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mo
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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.: 475 / 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: 3.91 Å3/Da / Density % sol: 68.53 %
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: Aug 18, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 212763 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.35→1.43 Å / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F6T

4f6t


Resolution: 1.35→9.986 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1773 9956 5.02 %Random
Rwork0.1603 ---
all0.1611 199787 --
obs0.1611 198513 99.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→9.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 165 475 4449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194283
X-RAY DIFFRACTIONf_angle_d1.95917
X-RAY DIFFRACTIONf_dihedral_angle_d15.0671618
X-RAY DIFFRACTIONf_chiral_restr0.101680
X-RAY DIFFRACTIONf_plane_restr0.009748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.39783260.40785450X-RAY DIFFRACTION87
1.3653-1.38130.39192990.38225846X-RAY DIFFRACTION93
1.3813-1.39810.3653090.34925955X-RAY DIFFRACTION96
1.3981-1.41580.34033260.31946133X-RAY DIFFRACTION98
1.4158-1.43440.28723340.28686192X-RAY DIFFRACTION99
1.4344-1.45390.27613350.26576222X-RAY DIFFRACTION100
1.4539-1.47470.25843180.24356302X-RAY DIFFRACTION100
1.4747-1.49660.24253150.22066264X-RAY DIFFRACTION100
1.4966-1.51990.23843460.20246296X-RAY DIFFRACTION100
1.5199-1.54470.20953310.18626264X-RAY DIFFRACTION100
1.5447-1.57130.20043390.17366267X-RAY DIFFRACTION100
1.5713-1.59970.19133110.16976286X-RAY DIFFRACTION100
1.5997-1.63040.18823230.16076317X-RAY DIFFRACTION100
1.6304-1.66350.17783250.15556295X-RAY DIFFRACTION100
1.6635-1.69950.18833060.14786357X-RAY DIFFRACTION100
1.6995-1.73880.15123340.1416269X-RAY DIFFRACTION100
1.7388-1.78210.17143490.13736303X-RAY DIFFRACTION100
1.7821-1.830.17153550.14216283X-RAY DIFFRACTION100
1.83-1.88350.1543530.13326297X-RAY DIFFRACTION100
1.8835-1.94380.15153470.13086338X-RAY DIFFRACTION100
1.9438-2.01280.14863490.12996309X-RAY DIFFRACTION100
2.0128-2.09270.15313410.13196371X-RAY DIFFRACTION100
2.0927-2.18690.15673240.13796371X-RAY DIFFRACTION100
2.1869-2.30090.15953500.13926370X-RAY DIFFRACTION100
2.3009-2.44310.163360.14146394X-RAY DIFFRACTION100
2.4431-2.62850.16053180.14646439X-RAY DIFFRACTION100
2.6285-2.88720.16983280.1486466X-RAY DIFFRACTION100
2.8872-3.29190.16193180.15256521X-RAY DIFFRACTION100
3.2919-4.09910.16183770.14656527X-RAY DIFFRACTION100
4.0991-9.98580.193340.1796853X-RAY DIFFRACTION100

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