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- PDB-1kuu: CRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM CONSERV... -

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Basic information

Entry
Database: PDB / ID: 1kuu
TitleCRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM CONSERVED PROTEIN MTH1020 REVEALS AN NTN-HYDROLASE FOLD
Componentsconserved protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved protein / 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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSaridakis, V. / Christendat, D. / Thygesen, A. / Arrowsmith, C.H. / Edwards, A.M. / Pai, E.F.
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2002
Title: CRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM CONSERVED PROTEIN MTH1020 REVEALS AN NTN-HYDROLASE FOLD
Authors: Saridakis, V. / Christendat, D. / Thygesen, A. / Arrowsmith, C.H. / Edwards, A.M. / Pai, E.F.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved protein


Theoretical massNumber of molelcules
Total (without water)21,8591
Polymers21,8591
Non-polymers00
Water57632
1
A: conserved protein

A: conserved protein

A: conserved protein

A: conserved protein


Theoretical massNumber of molelcules
Total (without water)87,4384
Polymers87,4384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Unit cell
Length a, b, c (Å)107.033, 107.033, 87.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein conserved protein


Mass: 21859.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter (archaea) / Genus: Methanothermobacter / Gene: MTH1020 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O27099
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14 % MPD, 0.2 M Mg Acetate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Christendat, D., (2000) J.Biol.Chem., 275, 24608.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 %MPD1reservoir
20.2 Mmagnesium acetate1reservoir
3100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 13025 / Num. obs: 13025 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 9 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 35.6
Reflection shellResolution: 2.2→2.34 Å / Rsym value: 0.374 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 113676
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.33 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SDMSdata reduction
SOLVEphasing
CNS1refinement
SDMSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→14.5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 245271.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 656 5.1 %RANDOM
Rwork0.229 ---
obs0.229 12746 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1196 Å2 / ksol: 0.349789 e/Å3
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2---2.57 Å20 Å2
3---5.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 0 32 1568
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 91 4.7 %
Rwork0.27 1865 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor obs: 0.27

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