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- PDB-9beo: Tungstate binding protein (Tungbindin) from Eubacterium limosum w... -

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Basic information

Entry
Database: PDB / ID: 9beo
TitleTungstate binding protein (Tungbindin) from Eubacterium limosum with 7.5 tungstates bound
ComponentsMolybdenum-pterin binding domain-containing protein
KeywordsMETAL BINDING PROTEIN / Tungsten / metal binding / metal oxyanion / hexamer
Function / homologyMolybdenum-pterin binding domain / Mop domain profile. / Transport-associated OB, type 1 / TOBE domain / molybdate ion transport / Molybdate/tungstate binding, C-terminal / TUNGSTATE(VI)ION / Molybdenum-pterin-binding protein
Function and homology information
Biological speciesEubacterium limosum (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.78 Å
AuthorsZhou, D. / Rose, J.P. / Chen, L. / Wang, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 136885 United States
CitationJournal: To Be Published
Title: Tungstate binding protein (Tungbindin) from Eubacterium limosum with 7.5 tungstates bound
Authors: Zhou, D. / Rose, J.P. / Chen, L. / Wang, B.C.
History
DepositionApr 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdenum-pterin binding domain-containing protein
B: Molybdenum-pterin binding domain-containing protein
C: Molybdenum-pterin binding domain-containing protein
D: Molybdenum-pterin binding domain-containing protein
E: Molybdenum-pterin binding domain-containing protein
F: Molybdenum-pterin binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,32914
Polymers49,3466
Non-polymers1,9838
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21160 Å2
ΔGint-132 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.752, 74.752, 156.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11E-265-

HOH

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Components

#1: Protein
Molybdenum-pterin binding domain-containing protein / Molybdopterin-binding protein / Tungstate binding protein / Tungbindin


Mass: 8224.404 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium limosum (bacteria) / Gene: C7955_103236, SAMN04515624_10415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0U3FVB3
#2: Chemical
ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: WO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→39.14 Å / Num. obs: 77439 / % possible obs: 96.5 % / Redundancy: 18 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.022 / Rrim(I) all: 0.1 / Net I/σ(I): 52.7
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 5 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.76 / Num. unique obs: 1071 / CC1/2: 0.86 / CC star: 0.962 / Rpim(I) all: 0.21 / Rrim(I) all: 0.497 / % possible all: 70.7

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→39.14 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1947 3715 4.8 %
Rwork0.1797 --
obs0.1804 77439 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 40 447 3499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093048
X-RAY DIFFRACTIONf_angle_d0.9954100
X-RAY DIFFRACTIONf_dihedral_angle_d15.171106
X-RAY DIFFRACTIONf_chiral_restr0.072519
X-RAY DIFFRACTIONf_plane_restr0.006511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.80.2548900.27711803X-RAY DIFFRACTION64
1.8-1.830.28041110.26422222X-RAY DIFFRACTION77
1.83-1.850.37651150.29882308X-RAY DIFFRACTION81
1.85-1.880.31220.2412430X-RAY DIFFRACTION84
1.88-1.910.28321260.24232565X-RAY DIFFRACTION90
1.91-1.940.2291420.212780X-RAY DIFFRACTION98
1.94-1.970.19951420.20442899X-RAY DIFFRACTION100
1.97-20.22721390.19472809X-RAY DIFFRACTION99
2-2.040.20311470.18962885X-RAY DIFFRACTION100
2.04-2.080.20171430.20542858X-RAY DIFFRACTION100
2.08-2.120.28911470.19942867X-RAY DIFFRACTION100
2.12-2.170.20361420.19332808X-RAY DIFFRACTION99
2.17-2.220.19661380.20592837X-RAY DIFFRACTION99
2.22-2.270.22211410.19072865X-RAY DIFFRACTION100
2.27-2.330.22961450.21882799X-RAY DIFFRACTION98
2.33-2.40.29731460.19892845X-RAY DIFFRACTION99
2.4-2.480.2341410.19612800X-RAY DIFFRACTION99
2.48-2.570.21911410.17682837X-RAY DIFFRACTION99
2.57-2.670.16021440.18382831X-RAY DIFFRACTION99
2.67-2.790.21711410.19682821X-RAY DIFFRACTION99
2.79-2.940.21331420.18722829X-RAY DIFFRACTION98
2.94-3.120.21611440.17322812X-RAY DIFFRACTION99
3.12-3.360.18781410.17042832X-RAY DIFFRACTION99
3.36-3.70.15221460.15592853X-RAY DIFFRACTION99
3.7-4.240.15011400.13362850X-RAY DIFFRACTION99
4.24-5.340.13951460.13772845X-RAY DIFFRACTION100
5.34-39.140.15331530.17382834X-RAY DIFFRACTION99

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