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- PDB-5o5w: Molybdenum storage protein room-temperature structure determined ... -

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Basic information

Entry
Database: PDB / ID: 5o5w
TitleMolybdenum storage protein room-temperature structure determined by serial millisecond crystallography
Components(Molybdenum storage protein subunit ...) x 2
KeywordsHYDROLASE / room-temperature / serial crystallography
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 / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8M0 / ADENOSINE-5'-TRIPHOSPHATE / Chem-M10 / MOLYBDENUM ATOM / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSteffen, B. / Weinert, T. / Ermler, U. / Standfuss, J.
CitationJournal: Nat Commun / Year: 2017
Title: Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons.
Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / ...Authors: Weinert, T. / Olieric, N. / Cheng, R. / Brunle, S. / James, D. / Ozerov, D. / Gashi, D. / Vera, L. / Marsh, M. / Jaeger, K. / Dworkowski, F. / Panepucci, E. / Basu, S. / Skopintsev, P. / Dore, A.S. / Geng, T. / Cooke, R.M. / Liang, M. / Prota, A.E. / Panneels, V. / Nogly, P. / Ermler, U. / Schertler, G. / Hennig, M. / Steinmetz, M.O. / Wang, M. / Standfuss, J.
History
DepositionJun 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,32529
Polymers57,7562
Non-polymers5,56927
Water3,207178
1
A: Molybdenum storage protein subunit alpha
B: Molybdenum storage protein subunit beta
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)189,97487
Polymers173,2676
Non-polymers16,70781
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 area37220 Å2
ΔGint-542 kcal/mol
Surface area46260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.350, 117.350, 233.350
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-308-

MO

21B-311-

MO

31B-456-

HOH

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Components

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Molybdenum storage protein subunit ... , 2 types, 2 molecules AB

#1: 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 genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: mosA, Avin_43200 / Production host: Escherichia coli (E. coli) / References: UniProt: P84308
#2: Protein Molybdenum storage protein subunit beta / MoSto subunit beta


Mass: 28378.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Gene: mosB, Avin_43210 / Production host: Escherichia coli (E. coli) / References: UniProt: P84253

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Non-polymers , 6 types, 205 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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-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
#7: Chemical...
ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mo
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0,1 M Na-Citrat pH 5,6 1,4 M NH4H2PO4 20 % Glycerol

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→24.2 Å / Num. obs: 110141 / % possible obs: 100 % / Redundancy: 765.4 % / Biso Wilson estimate: 29.42 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.29

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CrystFEL0.6.2data reduction
CrystFEL0.6.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6T

4f6t


Resolution: 1.7→24.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.067 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.07 / SU Rfree Cruickshank DPI: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.201 5090 4.95 %RANDOM
Rwork0.18 ---
obs-102901 98.6 %-
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1--4.7397 Å20 Å20 Å2
2---4.7397 Å20 Å2
3---9.4794 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 1.7→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 130 178 4100
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014012HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.155498HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1324SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes602HARMONIC5
X-RAY DIFFRACTIONt_it4012HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion17.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion523SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4679SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 330 5.03 %
Rwork0.289 6235 -
all0.289 6565 -
obs--86.48 %

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