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- PDB-2ntm: Crystal structure of PurO from Methanothermobacter thermoautotrophicus -

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Basic information

Entry
Database: PDB / ID: 2ntm
TitleCrystal structure of PurO from Methanothermobacter thermoautotrophicus
ComponentsIMP cyclohydrolase
KeywordsHYDROLASE / alpha-beta-beta-alpha NTN hydrolase fold
Function / homology
Function and homology information


IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
Inosine monophosphate cyclohydrolase-like / IMP cyclohydrolase / Inosine monophosphate cyclohydrolase-like / Inosine monophosphate cyclohydrolase-like superfamily / IMP cyclohydrolase-like protein / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKang, Y.N. / Tran, A. / White, R.H. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2007
Title: A novel function for the N-terminal nucleophile hydrolase fold demonstrated by the structure of an archaeal inosine monophosphate cyclohydrolase.
Authors: Kang, Y.N. / Tran, A. / White, R.H. / Ealick, S.E.
History
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMP cyclohydrolase
B: IMP cyclohydrolase
C: IMP cyclohydrolase
D: IMP cyclohydrolase


Theoretical massNumber of molelcules
Total (without water)96,1234
Polymers96,1234
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-19 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.277, 84.277, 124.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
IMP cyclohydrolase / Inosinicase / IMP synthetase


Mass: 24030.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: PurO / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O27099, IMP cyclohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25-30% MPD, 0.2M ammonium acetate, 0.1M sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 28, 2006
RadiationMonochromator: Multilayer confocal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 30485 / Num. obs: 29991 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 49.1 Å2 / Rsym value: 0.06 / Net I/σ(I): 27.41
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.91 / Num. unique all: 2984 / Rsym value: 0.375 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KUU

1kuu


Resolution: 2.6→36.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 299229.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2671 10 %RANDOM
Rwork0.225 ---
obs0.225 26707 88.2 %-
all-30487 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9211 Å2 / ksol: 0.308815 e/Å3
Displacement parametersBiso mean: 70.7 Å2
Baniso -1Baniso -2Baniso -3
1-14.63 Å214.27 Å20 Å2
2--14.63 Å20 Å2
3----29.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.6→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6168 0 0 14 6182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it2.771.5
X-RAY DIFFRACTIONc_mcangle_it4.072
X-RAY DIFFRACTIONc_scbond_it4.322
X-RAY DIFFRACTIONc_scangle_it5.712.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.412 375 10 %
Rwork0.362 3381 -
obs-3381 74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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