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- PDB-2ntk: Crystal structure of PurO/IMP from Methanothermobacter thermoauto... -

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Basic information

Entry
Database: PDB / ID: 2ntk
TitleCrystal structure of PurO/IMP 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
INOSINIC ACID / IMP cyclohydrolase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 ...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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,5168
Polymers96,1234
Non-polymers1,3934
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-12 kcal/mol
Surface area29440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.975, 85.975, 124.442
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: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
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: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97949
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 66529 / Num. obs: 65280 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.043 / Net I/σ(I): 26.99
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 6.27 / Num. unique all: 6678 / Rsym value: 0.215 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KUU

1kuu


Resolution: 2.03→27.45 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 862209.91 / 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
Rfree0.245 6017 10.1 %RANDOM
Rwork0.218 ---
obs0.218 59591 89.6 %-
all-66507 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.7496 Å2 / ksol: 0.412293 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.32 Å26.91 Å20 Å2
2--8.32 Å20 Å2
3----16.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.03→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6179 0 92 200 6471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it3.121.5
X-RAY DIFFRACTIONc_mcangle_it3.872
X-RAY DIFFRACTIONc_scbond_it4.832
X-RAY DIFFRACTIONc_scangle_it6.032.5
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 958 10.5 %
Rwork0.281 8195 -
obs-8195 82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4imp_pimp_p

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