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

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Basic information

Entry
Database: PDB / ID: 4ndq
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 / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / start from known model / Resolution: 1.751 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 / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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.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_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

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)62,29714
Polymers57,7562
Non-polymers4,54112
Water5,747319
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)186,89042
Polymers173,2676
Non-polymers13,62336
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 area36700 Å2
ΔGint-412 kcal/mol
Surface area45530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.150, 115.150, 234.500
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-304-

MO

21B-305-

MO

31A-304-

M10

41A-304-

M10

51A-307-

MO

DetailsAsymetric unit contains a dimer of subunit A and B; the biological unit is a hexamer generated from the dimer by the operations (1)x,y,z (2)-y,x-y,z (3)-x+y,-x,z (4)-x,-y,z+1/2 (5)y,-x+y,z+1/2 (6)x-y,x,z+1/2 (7)x,y,-z (8)x-y,-y,-z (9)-x,-x+y,-z (10)-y,-x,-z+1/2 (11)-x+y,y,-z+1/2 (12)x,x-y,-z+1/2

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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 (bacteria) / 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 / Details: ATCC 13705 / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: ATCC 13705 / References: UniProt: P84308

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Non-polymers , 6 types, 331 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-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.: 6 / Source method: obtained synthetically / Formula: Mo
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 3.89 Å3/Da / Density % sol: 68.34 %
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: Mar 21, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 91252 / Num. obs: 91252 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.6
Reflection shellResolution: 1.75→1.85 Å / % possible all: 99.2

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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: start from known model
Starting model: 4F6T

4f6t


Resolution: 1.751→9.997 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 4530 5 %Random
Rwork0.1789 ---
all0.1802 90659 --
obs0.1802 90659 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.751→9.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 145 319 4273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094139
X-RAY DIFFRACTIONf_angle_d1.7665692
X-RAY DIFFRACTIONf_dihedral_angle_d15.0721517
X-RAY DIFFRACTIONf_chiral_restr0.088651
X-RAY DIFFRACTIONf_plane_restr0.006720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7511-1.77090.37181250.31962167X-RAY DIFFRACTION76
1.7709-1.79160.36111600.30812812X-RAY DIFFRACTION100
1.7916-1.81340.35471560.31272869X-RAY DIFFRACTION99
1.8134-1.83620.3531380.29542819X-RAY DIFFRACTION99
1.8362-1.86020.30751520.27942875X-RAY DIFFRACTION99
1.8602-1.88550.29971340.26032855X-RAY DIFFRACTION99
1.8855-1.91220.31191340.25012856X-RAY DIFFRACTION99
1.9122-1.94060.22251510.24732849X-RAY DIFFRACTION99
1.9406-1.97070.24631520.21732866X-RAY DIFFRACTION99
1.9707-2.00270.23361390.21942870X-RAY DIFFRACTION99
2.0027-2.0370.21971350.21272885X-RAY DIFFRACTION99
2.037-2.07370.23861540.19922868X-RAY DIFFRACTION99
2.0737-2.11320.23981620.19742837X-RAY DIFFRACTION99
2.1132-2.15590.22491470.1862889X-RAY DIFFRACTION100
2.1559-2.20230.21341870.18112855X-RAY DIFFRACTION100
2.2023-2.2530.19521520.17482899X-RAY DIFFRACTION100
2.253-2.30870.21271520.17342880X-RAY DIFFRACTION99
2.3087-2.37030.23141470.16752893X-RAY DIFFRACTION100
2.3703-2.43910.2121450.17382916X-RAY DIFFRACTION100
2.4391-2.51660.22111510.17942886X-RAY DIFFRACTION99
2.5166-2.6050.19141520.16662894X-RAY DIFFRACTION99
2.605-2.70730.19911400.16812914X-RAY DIFFRACTION99
2.7073-2.82780.21991660.16992904X-RAY DIFFRACTION99
2.8278-2.97320.20381820.17162903X-RAY DIFFRACTION100
2.9732-3.1540.21221630.16812929X-RAY DIFFRACTION100
3.154-3.38870.18241390.16832951X-RAY DIFFRACTION99
3.3887-3.71370.17091550.15712929X-RAY DIFFRACTION98
3.7137-4.21540.15331480.14622974X-RAY DIFFRACTION99
4.2154-5.18470.16421470.14342996X-RAY DIFFRACTION98
5.1847-9.99690.18711650.1833089X-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)
10.6681-0.18110.32380.84040.10640.7399-0.03850.0581-0.0105-0.0725-0.01820.09980.0489-0.13060.00390.2099-0.0121-0.00610.1683-0.03520.193648.55917.323819.2274
23.0576-0.431-1.00122.5621.35672.3444-0.1539-0.1473-0.3070.1129-0.05130.24910.4394-0.20.17810.327-0.05320.00090.1927-0.05710.213143.69282.899811.7004
31.7-1.02070.3191.4725-0.6111.81510.015-0.0584-0.1025-0.04070.02540.2320.0018-0.24810.00220.1114-0.02190.00750.1865-0.01480.155237.371729.743747.6962
40.2947-0.0080.25620.5043-0.18111.22450.02010.0316-0.013-0.0896-0.01640.04890.0742-0.1395-0.00010.13220.0016-0.0030.1644-0.0190.165838.493328.588237.1288
54.609-0.448-0.89180.7908-0.49632.37690.01720.2059-0.2036-0.51960.18740.85230.487-0.8377-0.04230.2492-0.1314-0.10850.49630.00820.497218.614718.444140.3335
63.364-0.4964-1.05743.26382.78234.4394-0.095-0.0728-0.31220.21990.01920.16760.5311-0.31540.06960.1582-0.06380.00360.20620.030.17831.341718.346248.0632
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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