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

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Basic information

Entry
Database: PDB / ID: 4ndp
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: 1.6 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)63,83130
Polymers57,7562
Non-polymers6,07528
Water8,593477
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 area36050 Å2
ΔGint-402 kcal/mol
Surface area46740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.585, 115.585, 234.174
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-519-

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, 505 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.: 477 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.54 %
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

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: 1.55→50 Å / Num. all: 131006 / Num. obs: 131006 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.97 % / Net I/σ(I): 10.2
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 20119 / Rsym value: 0.72 / % possible all: 94

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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: 1.6→9.988 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 5994 5 %Random
Rwork0.1615 ---
all0.162 119879 --
obs0.1623 119879 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→9.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 165 477 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194201
X-RAY DIFFRACTIONf_angle_d1.9935781
X-RAY DIFFRACTIONf_dihedral_angle_d15.2591560
X-RAY DIFFRACTIONf_chiral_restr0.12659
X-RAY DIFFRACTIONf_plane_restr0.009731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61810.21682080.22583680X-RAY DIFFRACTION98
1.6181-1.63710.24722000.22123700X-RAY DIFFRACTION98
1.6371-1.65690.22621630.21833728X-RAY DIFFRACTION98
1.6569-1.67780.24882080.20973697X-RAY DIFFRACTION98
1.6778-1.69980.22031940.19833736X-RAY DIFFRACTION98
1.6998-1.7230.19871850.18763714X-RAY DIFFRACTION98
1.723-1.74750.19941880.18843724X-RAY DIFFRACTION98
1.7475-1.77340.1891810.17813736X-RAY DIFFRACTION98
1.7734-1.80090.20881860.17433761X-RAY DIFFRACTION99
1.8009-1.83030.1961820.17643724X-RAY DIFFRACTION99
1.8303-1.86170.16582360.16523727X-RAY DIFFRACTION99
1.8617-1.89530.22131850.16683769X-RAY DIFFRACTION99
1.8953-1.93150.19022120.16593722X-RAY DIFFRACTION99
1.9315-1.97060.18961790.16533759X-RAY DIFFRACTION99
1.9706-2.01310.17741800.15933788X-RAY DIFFRACTION99
2.0131-2.05960.18491990.15843798X-RAY DIFFRACTION99
2.0596-2.11060.18742130.15943762X-RAY DIFFRACTION99
2.1106-2.16710.16922190.15393764X-RAY DIFFRACTION99
2.1671-2.23020.17691850.15033810X-RAY DIFFRACTION99
2.2302-2.30130.18522000.15363791X-RAY DIFFRACTION99
2.3013-2.38250.1621930.14713809X-RAY DIFFRACTION99
2.3825-2.47650.15952000.15763821X-RAY DIFFRACTION99
2.4765-2.58730.16092490.15033790X-RAY DIFFRACTION100
2.5873-2.72110.15172080.15243829X-RAY DIFFRACTION100
2.7211-2.88780.16331850.15143900X-RAY DIFFRACTION100
2.8878-3.10450.16412110.15253869X-RAY DIFFRACTION100
3.1045-3.40560.16252010.15563911X-RAY DIFFRACTION100
3.4056-3.8730.16452090.14613929X-RAY DIFFRACTION100
3.873-4.78840.15872180.14163983X-RAY DIFFRACTION100
4.7884-9.98840.21852170.19334154X-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)
10.8474-0.0427-0.06110.77910.10171.0999-0.00510.11690.0246-0.1173-0.00270.1107-0.0022-0.15180.00530.1531-0.0098-0.0190.1163-0.02910.146348.910917.487118.7003
24.3697-0.5571-1.04654.14372.44261.5603-0.231-0.299-0.66920.4445-0.00780.2480.58110.00960.20050.3674-0.02780.02570.2213-0.00650.205844.4072-1.335413.3368
34.9477-1.4891-2.11093.50532.12172.5491-0.0468-0.0112-0.2239-0.0599-0.09920.31040.1102-0.1970.16280.2142-0.0161-0.04390.1307-0.0450.161443.68997.19879.6996
40.6189-0.1890.36080.4607-0.4011.9889-0.0065-0.064-0.0136-0.00810.01540.0838-0.0001-0.1962-0.0120.098-0.0173-0.00110.1375-0.00430.148936.875730.665341.7078
50.8190.12010.86610.48350.34222.04050.04470.0464-0.0497-0.06280.0052-0.02930.0380.0111-0.05680.1068-0.00110.01010.12120.00090.14143.470829.73536.112
62.5875-0.1223-0.2611.9730.35731.5229-0.05880.0341-0.2479-0.07090.03440.38230.1988-0.3838-0.02090.1255-0.0568-0.0050.19670.01060.191328.301519.746144.4017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 180 )
2X-RAY DIFFRACTION2chain 'B' and (resid 181 through 226 )
3X-RAY DIFFRACTION3chain 'B' and (resid 227 through 270 )
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 169 )
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 276 )

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