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- PDB-2cu0: Crystal structure of inosine-5'-monophosphate dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 2cu0
TitleCrystal structure of inosine-5'-monophosphate dehydrogenase from Pyrococcus horikoshii OT3
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / Pyrococcus horikoshii OT3 / inosine-5'-monophosphate dehydrogenase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP 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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Aldolase class I ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / 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
XANTHOSINE-5'-MONOPHOSPHATE / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAsada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of inosine-5'-monophosphate dehydrogenase from Pyrococcus horikoshii OT3
Authors: Asada, Y. / Kunishima, N.
History
DepositionMay 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)106,7394
Polymers106,0092
Non-polymers7302
Water6,738374
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


Theoretical massNumber of molelcules
Total (without water)213,4798
Polymers212,0184
Non-polymers1,4614
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 area23600 Å2
ΔGint-164 kcal/mol
Surface area49210 Å2
MethodPISA, PQS
2
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)213,4798
Polymers212,0184
Non-polymers1,4614
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 area22830 Å2
ΔGint-148 kcal/mol
Surface area49460 Å2
MethodPISA, PQS
3
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)426,95816
Polymers424,0368
Non-polymers2,9228
Water1448
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 area53200 Å2
ΔGint-334 kcal/mol
Surface area91900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.666, 123.666, 130.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-1150-

HOH

21A-1156-

HOH

31A-1183-

HOH

41B-1167-

HOH

51B-1192-

HOH

DetailsThe biological assembly is tetramer generated from the chain A in the asymmetric unit by the operations: x,y,z : -x,-y,z : -y,x,z : y,-x ,z / The biological assembly is tetramer generated from the chain B in the asymmetric unit by the operations: x,y,z : -x,-y,z : -y,x,z : y,-x ,z

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Components

#1: Protein Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPDH / IMPD


Mass: 53004.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58045, IMP dehydrogenase
#2: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE / Xanthosine monophosphate


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 9.6
Details: 50 %(v/v) PEG-200 CHES, pH 9.6, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 26, 2004
RadiationMonochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 56527 / Num. obs: 56527 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 33.473 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 4.09 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZFJ.pdb

1zfj


Resolution: 2.1→29.23 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2790 -RANDOM
Rwork0.205 ---
all0.206 56526 --
obs0.206 56526 99.7 %-
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.7 Å20 Å20 Å2
2---6.7 Å20 Å2
3---13.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 48 374 5820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.285 314 -
Rwork0.26 --
obs--94.9 %

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