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- PDB-1i36: Structure of Conserved Protein MTH1747 of Unknown Function Reveal... -

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Basic information

Entry
Database: PDB / ID: 1i36
TitleStructure of Conserved Protein MTH1747 of Unknown Function Reveals Structural Similarity with 3-Hydroxyacid Dehydrogenases
ComponentsCONSERVED HYPOTHETICAL PROTEIN MTH1747
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NADP binding domain / protein NADP complex / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Phosphogluconate dehydrogenase, NAD-binding, putative, C-terminal / Domain of unknown function (DUF1932) / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Phosphogluconate dehydrogenase, NAD-binding, putative, C-terminal / Domain of unknown function (DUF1932) / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Conserved protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKorolev, S.V. / Dementieva, I.S. / Christendat, D. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: to be published
Title: STRUCTURAL SIMILARITIES OF MTH1747 HYPOTHETICAL PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH 3-HYDROXYACID DEHYDROGENASES
Authors: Korolev, S.V. / Dementieva, I.S. / Christendat, D. / Edwards, A. / Joachimiak, A.
History
DepositionFeb 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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: CONSERVED HYPOTHETICAL PROTEIN MTH1747
B: CONSERVED HYPOTHETICAL PROTEIN MTH1747
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5254
Polymers58,0392
Non-polymers1,4872
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-44 kcal/mol
Surface area22310 Å2
MethodPISA
2
A: CONSERVED HYPOTHETICAL PROTEIN MTH1747
B: CONSERVED HYPOTHETICAL PROTEIN MTH1747
hetero molecules

A: CONSERVED HYPOTHETICAL PROTEIN MTH1747
B: CONSERVED HYPOTHETICAL PROTEIN MTH1747
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,0518
Polymers116,0774
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area15300 Å2
ΔGint-93 kcal/mol
Surface area43070 Å2
MethodPISA
3
A: CONSERVED HYPOTHETICAL PROTEIN MTH1747
B: CONSERVED HYPOTHETICAL PROTEIN MTH1747
hetero molecules

A: CONSERVED HYPOTHETICAL PROTEIN MTH1747
B: CONSERVED HYPOTHETICAL PROTEIN MTH1747
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,0518
Polymers116,0774
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area14820 Å2
ΔGint-88 kcal/mol
Surface area43550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.870, 123.457, 133.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CONSERVED HYPOTHETICAL PROTEIN MTH1747


Mass: 29019.299 Da / Num. of mol.: 2 / Mutation: M1L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: MTH1747 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: O27779
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, sodium acetate, mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97921,0.97935,1.016273
SYNCHROTRONAPS 19-ID20.99187
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDSep 21, 1999
CUSTOM-MADE2CCDMay 25, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979351
31.0162731
40.991871
ReflectionResolution: 2→30 Å / Num. all: 53318 / Num. obs: 52782 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 32
Reflection shellResolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
d*TREKdata scaling
HKL-2000data reduction
SOLVEphasing
SHARPphasing
Omodel building
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→23.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 398286.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2585 5.1 %RANDOM
Rwork0.203 ---
obs0.203 51168 95.9 %-
all-53318 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.92 Å20 Å20 Å2
2--1.58 Å20 Å2
3----7.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-25 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→23.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 96 421 4443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.72
X-RAY DIFFRACTIONc_mcbond_it1.861.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it2.952
X-RAY DIFFRACTIONc_scangle_it4.522.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.255 280 5.6 %
Rwork0.237 4686 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAP_xplor_par.txtNAP_XPLOR_TOP.txt
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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