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- PDB-2ogx: The crystal structure of the molybdenum storage protein from Azot... -

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Basic information

Entry
Database: PDB / ID: 2ogx
TitleThe crystal structure of the molybdenum storage protein from Azotobacter vinelandii loaded with polyoxotungstates (WSto)
Components(Molybdenum storage protein subunit ...) x 2
KeywordsMETAL BINDING PROTEIN / open alpha/beta structure
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
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / : / TRI-TUNGSTEN(VI) OXIDE COMPLEX / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSchemberg, J. / Warkentin, E. / Ermler, U.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: Towards Biological Supramolecular Chemistry: A Variety of Pocket-Templated, Individual Metal Oxide Cluster Nucleations in the Cavity of a Mo/W-Storage Protein.
Authors: Schemberg, J. / Schneider, K. / Demmer, U. / Warkentin, E. / Muller, A. / Ermler, U.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)63,98130
Polymers58,2712
Non-polymers5,70928
Water7,044391
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)191,94290
Polymers174,8146
Non-polymers17,12884
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 area39880 Å2
ΔGint-674 kcal/mol
Surface area45370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)114.400, 114.400, 233.700
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-2008-

WO3

21B-2011-

W

DetailsThe biological assembly is a heterohexamer, (AB)3, generated from the heterodimer AB by the three fold axis: -y+1, x-y, z, and y-x+1, -x+1, z, respectively.

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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 alpha subunit / MoSto subunit alpha


Mass: 29564.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DSMZ 366 / References: UniProt: P84308
#2: Protein Molybdenum storage protein subunit beta / Mo storage protein subunit beta / MoSto subunit beta


Mass: 28707.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: DSMZ 366 / References: UniProt: P84253

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Non-polymers , 6 types, 419 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-WO3 / TRI-TUNGSTEN(VI) OXIDE COMPLEX


Mass: 759.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O13W3
#5: 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
#6: Chemical...
ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: W
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M MOPS, 0.05M sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9787
SYNCHROTRONSLS X10SA20.98
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDApr 24, 2005mirrors
MARMOSAIC 225 mm CCD2CCDApr 24, 2005mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.981
ReflectionResolution: 1.6→10 Å / Num. all: 107052 / Num. obs: 107052 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 6.5 / Net I/σ(I): 10.3
Reflection shellResolution: 0→0 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2 / Rsym value: 5.15 / % possible all: 82.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.905 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19645 5682 5 %RANDOM
Rwork0.17295 ---
all0.17414 107052 --
obs0.17414 107052 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 70 391 4273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224010
X-RAY DIFFRACTIONr_angle_refined_deg1.911.9955466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74922.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52315650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7431538
X-RAY DIFFRACTIONr_chiral_restr0.1270.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022997
X-RAY DIFFRACTIONr_nbd_refined0.2260.22107
X-RAY DIFFRACTIONr_nbtor_refined0.3230.22816
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2415
X-RAY DIFFRACTIONr_metal_ion_refined0.370.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.2138
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.229
X-RAY DIFFRACTIONr_mcbond_it1.2921.52606
X-RAY DIFFRACTIONr_mcangle_it2.02824122
X-RAY DIFFRACTIONr_scbond_it3.06331518
X-RAY DIFFRACTIONr_scangle_it4.6994.51343
LS refinement shellResolution: 1.603→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 334 -
Rwork0.259 6058 -
obs--76.21 %
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)
10.3605-0.2012-0.06030.83440.02240.8431-0.0127-0.0063-0.0567-0.0010.0050.12480.0803-0.15110.0077-0.0395-0.01710.00280.00350.001-0.016433.9923.16343.207
20.4214-0.1259-0.1740.48070.39870.8343-0.02620.0519-0.0794-0.0408-0.02270.05880.0731-0.04030.04890.0302-0.0097-0.0049-0.0415-0.0434-0.026747.6479.29113.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 8031 - 80
2X-RAY DIFFRACTION1AA131 - 276131 - 276
3X-RAY DIFFRACTION2BB32 - 8032 - 80
4X-RAY DIFFRACTION2BB131 - 270131 - 270

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