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- PDB-8p4q: Structure of the IMP dehydrogenase related protein GUAB3 from Syn... -

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Basic information

Entry
Database: PDB / ID: 8p4q
TitleStructure of the IMP dehydrogenase related protein GUAB3 from Synechocystis PCC 6803
ComponentsIMP dehydrogenase subunit
KeywordsBIOSYNTHETIC PROTEIN / IMP dehydrogenase related protein GUAB3 complexed to IMP-XMP
Function / homology
Function and homology information


IMP dehydrogenase activity / purine nucleotide biosynthetic process / nucleotide binding
Similarity search - Function
IMP dehydrogenase-related 2 / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Aldolase-type TIM barrel
Similarity search - Domain/homology
INOSINIC ACID / XANTHOSINE-5'-MONOPHOSPHATE / IMP dehydrogenase subunit
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsHernandez-Gomez, A. / Fernandez-Justel, D. / Buey, R.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-109671GB-I00 Spain
CitationJournal: Structure / Year: 2023
Title: GuaB3, an overlooked enzyme in cyanobacteria's toolbox that sheds light on IMP dehydrogenase evolution.
Authors: Hernandez-Gomez, A. / Irisarri, I. / Fernandez-Justel, D. / Pelaez, R. / Jimenez, A. / Revuelta, J.L. / Balsera, M. / Buey, R.M.
History
DepositionMay 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMP dehydrogenase subunit
B: IMP dehydrogenase subunit
C: IMP dehydrogenase subunit
D: IMP dehydrogenase subunit
E: IMP dehydrogenase subunit
F: IMP dehydrogenase subunit
G: IMP dehydrogenase subunit
H: IMP dehydrogenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,13824
Polymers324,4318
Non-polymers5,70716
Water28,9141605
1
A: IMP dehydrogenase subunit
B: IMP dehydrogenase subunit
C: IMP dehydrogenase subunit
D: IMP dehydrogenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,06912
Polymers162,2154
Non-polymers2,8548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: IMP dehydrogenase subunit
F: IMP dehydrogenase subunit
G: IMP dehydrogenase subunit
H: IMP dehydrogenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,06912
Polymers162,2154
Non-polymers2,8548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.980, 131.680, 182.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid -2 through 2 and (name N...
d_2ens_1(chain "B" and (resid -2 or (resid -1 through 2...
d_3ens_1(chain "C" and (resid -2 or (resid -1 through 2...
d_4ens_1(chain "D" and (resid -2 through 32 or (resid 33...
d_5ens_1(chain "E" and (resid -2 or (resid -1 through 2...
d_6ens_1(chain "F" and (resid -2 or (resid -1 through 2...
d_7ens_1(chain "G" and (resid -2 or (resid -1 through 2...
d_8ens_1(chain "H" and (resid -2 or (resid -1 through 2...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYLEUA1 - 69
d_12ens_1GLULEUA71 - 108
d_13ens_1GLNPROA110 - 174
d_14ens_1GLUALAA176 - 222
d_15ens_1THRLYSA224 - 388
d_21ens_1GLYLEUC1 - 69
d_22ens_1GLULEUC71 - 108
d_23ens_1GLNPROC110 - 174
d_24ens_1GLUALAC176 - 222
d_25ens_1THRLYSC224 - 388
d_31ens_1GLYLEUE1 - 69
d_32ens_1GLULEUE71 - 108
d_33ens_1GLNPROE110 - 174
d_34ens_1GLUALAE176 - 222
d_35ens_1THRLYSE224 - 388
d_41ens_1GLYLEUG1 - 69
d_42ens_1GLULEUG71 - 108
d_43ens_1GLNPROG110 - 174
d_44ens_1GLUALAG176 - 222
d_45ens_1THRLYSG224 - 388
d_51ens_1GLYLEUI1 - 69
d_52ens_1GLULEUI71 - 108
d_53ens_1GLNPROI110 - 174
d_54ens_1GLUALAI178 - 224
d_55ens_1THRLYSI226 - 390
d_61ens_1GLYLEUK1 - 69
d_62ens_1GLULEUK71 - 108
d_63ens_1GLNPROK110 - 174
d_64ens_1GLUALAK176 - 222
d_65ens_1THRLYSK224 - 388
d_71ens_1GLYLEUM1 - 69
d_72ens_1GLULEUM71 - 108
d_73ens_1GLNPROM110 - 174
d_74ens_1GLUALAM177 - 223
d_75ens_1THRLYSM225 - 389
d_81ens_1GLYLEUO1 - 69
d_82ens_1GLULEUO71 - 108
d_83ens_1GLNPROO110 - 174
d_84ens_1GLUALAO178 - 224
d_85ens_1THRLYSO226 - 390

NCS oper:
IDCodeMatrixVector
1given(0.0104300490992, 0.995922626533, -0.0896065624538), (-0.999536698856, 0.00782137384363, -0.0294145159894), (-0.0285937355986, 0.089871842477, 0.995542791754)-47.8535354406, -47.854583141, -1.29391418958
2given(-0.991081174188, -0.00288404525362, -0.13322833202), (-0.00646279507503, -0.997549098939, 0.069670851048), (-0.133102736447, 0.0699104962714, 0.988633493293)-95.9566517798, 0.452521489032, -6.50022134441
3given(-0.00105827716248, -0.999384382935, -0.0350675804052), (0.995596898224, -0.0043399297276, 0.0936374992066), (-0.0937320451988, -0.0348140798527, 0.994988584631)-47.9012114706, 48.3707996806, -4.47393263057
4given(0.983483210243, 0.128333248032, 0.127637583101), (0.129121727392, -0.991626501279, 0.00211222094466), (0.126839878136, 0.0144034513747, -0.991818625507)-0.530728220853, 6.83043817993, 2.42944217818
5given(0.121446166318, -0.986529079632, 0.109595637351), (-0.98625040472, -0.132398613489, -0.0988976558656), (0.112075723849, -0.0960780005307, -0.98904400809)-41.6027884584, -47.1494839675, 1.8435855466
6given(-0.993328479718, -0.115292120281, 0.00250167579013), (-0.11507510414, 0.989581237122, -0.0865256929714), (0.00750011917816, -0.0862363156579, -0.996246478575)-95.903936611, -5.62769297176, -3.12467520281
7given(-0.126505510824, 0.991504716851, 0.0302448705319), (0.991823492814, 0.125911913075, 0.0207930096141), (0.0168081776006, 0.0326280034335, -0.999326222291)-54.2666240372, 48.0482125257, -3.0072576026

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Components

#1: Protein
IMP dehydrogenase subunit


Mass: 40553.863 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: guaB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73853
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1605 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown in the presence of XMP and NAD+ in mother liquor from the condition 1-10 of the commercial screen Morpheus (Molecular Dimensions), which consists of a salt mixture (0.03M ...Details: Crystals were grown in the presence of XMP and NAD+ in mother liquor from the condition 1-10 of the commercial screen Morpheus (Molecular Dimensions), which consists of a salt mixture (0.03M Magnesium chloride hexahydrate and 0.03M Calcium chloride dihydrate), a precipitant mix (20% v/v Ethylene glycol and 10 % w/v PEG 8000), and 0.1M of a buffer system (Tris-base, Bicine) adjusted at pH 8.5. Initial concentrations: Protein = 12.5 mg/mL XMP = 3 mM NAD = 3 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979263470491 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979263470491 Å / Relative weight: 1
ReflectionResolution: 1.88→49.04 Å / Num. obs: 219243 / % possible obs: 90.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 31.06 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.073 / Net I/σ(I): 14.21
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 1.18 % / Mean I/σ(I) obs: 0.67 / Num. unique obs: 7407 / CC1/2: 0.55 / Rrim(I) all: 0.806 / % possible all: 35.3

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4933refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→49.04 Å / SU ML: 0.2062 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 11046 5.04 %
Rwork0.1784 208127 -
obs0.1793 219173 90.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.88 Å2
Refinement stepCycle: LAST / Resolution: 1.88→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22122 0 376 1606 24104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004822955
X-RAY DIFFRACTIONf_angle_d0.68431372
X-RAY DIFFRACTIONf_chiral_restr0.05023833
X-RAY DIFFRACTIONf_plane_restr0.00544015
X-RAY DIFFRACTIONf_dihedral_angle_d11.73278214
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.262495333697
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.259640594065
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.344387391215
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.285039668707
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.246911998391
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.266989932337
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.238789448413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.35821450.39092372X-RAY DIFFRACTION31.57
1.9-1.920.38191490.37662887X-RAY DIFFRACTION37.95
1.92-1.950.39292100.35533914X-RAY DIFFRACTION51.48
1.95-1.970.37413050.3345514X-RAY DIFFRACTION72.38
1.97-20.33373390.30825930X-RAY DIFFRACTION78.25
2-2.020.32323620.28616106X-RAY DIFFRACTION80.69
2.02-2.050.29694120.25966543X-RAY DIFFRACTION86.72
2.05-2.080.25873760.23496885X-RAY DIFFRACTION90.72
2.08-2.110.25143610.2197056X-RAY DIFFRACTION92.82
2.12-2.150.23993690.21227310X-RAY DIFFRACTION95.43
2.15-2.190.22224020.2027489X-RAY DIFFRACTION97.93
2.19-2.230.21774060.19357563X-RAY DIFFRACTION99.02
2.23-2.270.22213900.19627555X-RAY DIFFRACTION99.35
2.27-2.320.22133710.18937678X-RAY DIFFRACTION99.85
2.32-2.370.2163750.17617651X-RAY DIFFRACTION99.93
2.37-2.420.2274220.17987659X-RAY DIFFRACTION99.95
2.42-2.480.20084270.1787615X-RAY DIFFRACTION99.9
2.48-2.550.19543960.1747624X-RAY DIFFRACTION99.88
2.55-2.620.20224370.17497633X-RAY DIFFRACTION99.94
2.62-2.710.1914300.17427610X-RAY DIFFRACTION99.88
2.71-2.810.19794050.17027678X-RAY DIFFRACTION99.88
2.81-2.920.19523830.17647713X-RAY DIFFRACTION99.84
2.92-3.050.20263980.18747663X-RAY DIFFRACTION99.78
3.05-3.210.19493840.18557713X-RAY DIFFRACTION99.69
3.21-3.410.17893970.16937665X-RAY DIFFRACTION99.64
3.41-3.680.17843840.16577743X-RAY DIFFRACTION99.58
3.68-4.050.15563920.14967735X-RAY DIFFRACTION99.67
4.05-4.630.15043800.13137793X-RAY DIFFRACTION99.49
4.63-5.830.16254060.14937839X-RAY DIFFRACTION99.53
5.83-49.040.19154330.19027991X-RAY DIFFRACTION98.63

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