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- PDB-7oj1: Bacillus subtilis IMPDH in complex with Ap4A -

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Basic information

Entry
Database: PDB / ID: 7oj1
TitleBacillus subtilis IMPDH in complex with Ap4A
Components(Inosine-5'-monophosphate dehydrogenase) x 2
KeywordsSIGNALING PROTEIN / IMP Dehydrogenase / Delta CBS mutant
Function / homologyBIS(ADENOSINE)-5'-TETRAPHOSPHATE
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsGiammarinaro, P.I. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Microbiol / Year: 2022
Title: Diadenosine tetraphosphate regulates biosynthesis of GTP in Bacillus subtilis.
Authors: Giammarinaro, P.I. / Young, M.K.M. / Steinchen, W. / Mais, C.N. / Hochberg, G. / Yang, J. / Stevenson, D.M. / Amador-Noguez, D. / Paulus, A. / Wang, J.D. / Bange, G.
History
DepositionMay 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2186
Polymers88,4972
Non-polymers1,7214
Water63135
1
A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

A: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

B: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,87224
Polymers353,9878
Non-polymers6,88616
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
crystal symmetry operation5_544x+1/2,y-1/2,z-1/21
crystal symmetry operation6_544-x+1/2,-y-1/2,z-1/21
crystal symmetry operation7_544-y+1/2,x-1/2,z-1/21
crystal symmetry operation8_544y+1/2,-x-1/2,z-1/21
Buried area42390 Å2
ΔGint-246 kcal/mol
Surface area137730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.750, 133.750, 149.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase


Mass: 42969.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: guaB, B4122_3662, B4417_3411, ETA10_00070, ETK61_00070, GII81_00070, SC09_Contig28orf00345
Production host: Escherichia coli BL21(DE3) (bacteria) / References: IMP dehydrogenase
#2: Protein Inosine-5'-monophosphate dehydrogenase


Mass: 45527.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: guaB, B4122_3662, B4417_3411, ETA10_00070, ETK61_00070, GII81_00070, SC09_Contig28orf00345
Production host: Escherichia coli BL21(DE3) (bacteria) / References: IMP dehydrogenase
#3: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE


Mass: 836.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O19P4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Acetate pH 4.5, 40% v/v 1,2-Propanediol, 20% Glycerol.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978561 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978561 Å / Relative weight: 1
ReflectionResolution: 2.44→99.73 Å / Num. obs: 89450 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.064 / Rrim(I) all: 0.129 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.44-2.523.90.4641753044740.6490.2640.5362.699.8
9.77-99.733.60.0728347830.9870.0420.08214.899.3

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQW

4dqw


Resolution: 2.44→66.88 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.51 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2872 4664 5.21 %
Rwork0.2682 --
obs0.2692 89450 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→66.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6112 0 108 35 6255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096264
X-RAY DIFFRACTIONf_angle_d1.0778475
X-RAY DIFFRACTIONf_dihedral_angle_d20.8562321
X-RAY DIFFRACTIONf_chiral_restr0.0651037
X-RAY DIFFRACTIONf_plane_restr0.0051056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.470.40311800.38022823X-RAY DIFFRACTION94
2.47-2.50.39391530.36762813X-RAY DIFFRACTION94
2.5-2.530.39141310.362964X-RAY DIFFRACTION94
2.53-2.560.32541540.35442811X-RAY DIFFRACTION94
2.56-2.60.35841460.34372844X-RAY DIFFRACTION94
2.6-2.630.31161520.34212825X-RAY DIFFRACTION93
2.63-2.670.42741050.32992914X-RAY DIFFRACTION93
2.67-2.710.34931730.32212755X-RAY DIFFRACTION93
2.71-2.750.3091800.30832785X-RAY DIFFRACTION92
2.75-2.80.32881660.29192698X-RAY DIFFRACTION89
2.8-2.840.31741490.29442551X-RAY DIFFRACTION85
2.84-2.90.28181370.29492697X-RAY DIFFRACTION89
2.9-2.950.40281680.30482920X-RAY DIFFRACTION95
2.95-3.010.29751640.312906X-RAY DIFFRACTION95
3.01-3.080.33171670.28272839X-RAY DIFFRACTION95
3.08-3.150.28381850.27782882X-RAY DIFFRACTION95
3.15-3.230.30741420.27032856X-RAY DIFFRACTION94
3.23-3.310.28071310.27242858X-RAY DIFFRACTION93
3.31-3.410.32971610.25792763X-RAY DIFFRACTION90
3.41-3.520.31581620.26632656X-RAY DIFFRACTION87
3.52-3.650.29831580.25922854X-RAY DIFFRACTION94
3.65-3.790.28141310.25212920X-RAY DIFFRACTION96
3.79-3.970.29591500.24742878X-RAY DIFFRACTION96
3.97-4.180.24521720.23042901X-RAY DIFFRACTION95
4.18-4.440.26831610.23192829X-RAY DIFFRACTION93
4.44-4.780.2241220.24392745X-RAY DIFFRACTION89
4.78-5.260.27721640.24722914X-RAY DIFFRACTION96
5.26-6.020.27971760.29022904X-RAY DIFFRACTION96
6.02-7.580.30711590.27232778X-RAY DIFFRACTION92
7.59-66.880.2051650.22842903X-RAY DIFFRACTION95

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