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- PDB-7xlo: Crystal Structure of the Catalytic Domain of Inosine Monophosphat... -

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Basic information

Entry
Database: PDB / ID: 7xlo
TitleCrystal Structure of the Catalytic Domain of Inosine Monophosphate Dehydrogenase (IMPDH) from Methanocaldococcus jannaschii
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / IMPDH TIM / Catalytic domain / alpha and beta proteins (a/b) / TIM beta/alpha-barrel
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBellur, A. / Sharma, P. / Balaram, H.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Science and Engineering Research Board (SERB) India
CitationJournal: To Be Published
Title: Crystal Structure of the Catalytic Domain of Inosine Monophosphate Dehydrogenase (IMPDH) from Methanocaldococcus jannaschii
Authors: Bellur, A. / Sharma, P. / Balaram, H.
History
DepositionApr 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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


Theoretical massNumber of molelcules
Total (without water)84,5082
Polymers84,5082
Non-polymers00
Water2,972165
1
A: Inosine-5'-monophosphate dehydrogenase

A: Inosine-5'-monophosphate dehydrogenase

A: Inosine-5'-monophosphate dehydrogenase

A: Inosine-5'-monophosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)169,0154
Polymers169,0154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15480 Å2
ΔGint-114 kcal/mol
Surface area50340 Å2
MethodPISA
2
B: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase

B: Inosine-5'-monophosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)169,0154
Polymers169,0154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area14080 Å2
ΔGint-104 kcal/mol
Surface area49220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.650, 97.650, 168.220
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 / IMP dehydrogenase / IMPD / IMPDH


Mass: 42253.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: guaB, MJ1616 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q59011, IMP dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 297 K / Method: microbatch
Details: 0.05 M magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, 30% v/v polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 31, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→53.37 Å / Num. obs: 24178 / % possible obs: 100 % / Redundancy: 4.4 % / CC1/2: 0.845 / Net I/σ(I): 4
Reflection shellResolution: 2.6→2.74 Å / Num. unique obs: 24178 / CC1/2: 0.845

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cu0

2cu0


Resolution: 2.6→53.37 Å / Cor.coef. Fo:Fc: 0.827 / Cor.coef. Fo:Fc free: 0.806 / SU B: 15.822 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R: 0.843 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27606 1233 5.1 %RANDOM
Rwork0.25416 ---
obs0.25525 22945 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.675 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2---0.6 Å20 Å2
3---1.2 Å2
Refinement stepCycle: 1 / Resolution: 2.6→53.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 0 165 4921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134829
X-RAY DIFFRACTIONr_bond_other_d0.0050.0174786
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6316518
X-RAY DIFFRACTIONr_angle_other_deg1.3651.58111063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0595637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02923.5200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40315848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2281523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025358
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02871
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7621.6742587
X-RAY DIFFRACTIONr_mcbond_other0.7621.6742586
X-RAY DIFFRACTIONr_mcangle_it1.3362.5043211
X-RAY DIFFRACTIONr_mcangle_other1.3362.5043212
X-RAY DIFFRACTIONr_scbond_it0.6141.7772242
X-RAY DIFFRACTIONr_scbond_other0.6131.7772240
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0992.6263307
X-RAY DIFFRACTIONr_long_range_B_refined3.17320.1855200
X-RAY DIFFRACTIONr_long_range_B_other3.16520.2135183
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 100 -
Rwork0.36 1683 -
obs--100 %

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