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- PDB-3x2e: A thermophilic hydrolase -

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Basic information

Entry
Database: PDB / ID: 3x2e
TitleA thermophilic hydrolase
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / NAD+ binding
Function / homology
Function and homology information


adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZheng, Y. / Ko, T.P. / Huang, C.H.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structures of S-adenosylhomocysteine hydrolase from the thermophilic bacterium Thermotoga maritima.
Authors: Zheng, Y. / Chen, C.C. / Ko, T.P. / Xiao, X. / Yang, Y. / Huang, C.H. / Qian, G. / Shao, W. / Guo, R.T.
History
DepositionDec 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,8888
Polymers183,2264
Non-polymers2,6624
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21560 Å2
ΔGint-114 kcal/mol
Surface area56120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.331, 111.999, 164.888
Angle α, β, γ (deg.)90.00, 103.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-665-

HOH

21C-634-

HOH

31D-601-

HOH

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Components

#1: Protein
Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 45806.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: ahcY, sahh, TM_0172 / Plasmid: pHsh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O51933, adenosylhomocysteinase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 4.3 M NaNO3, 0.1 M NaAc, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→25 Å / Num. obs: 43417 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 15.2
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4291 / % possible all: 98.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B3R

1b3r


Resolution: 2.85→25 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 2043 4.6 %random
Rwork0.2288 ---
obs-40772 --
Solvent computationBsol: 30.1495 Å2
Displacement parametersBiso max: 147.74 Å2 / Biso mean: 78.5835 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.554 Å2-0 Å27.876 Å2
2--33.358 Å20 Å2
3----33.912 Å2
Refinement stepCycle: LAST / Resolution: 2.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12464 0 176 353 12993
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5171.5
X-RAY DIFFRACTIONc_scbond_it2.3992.5
X-RAY DIFFRACTIONc_mcangle_it2.6812.5
X-RAY DIFFRACTIONc_scangle_it3.7533.5
LS refinement shellResolution: 2.85→2.95 Å / Rfactor Rfree: 0.476 / Rfactor Rwork: 0.42
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2NAI.param

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