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- PDB-3lwg: Crystal structure of HP0420-homologue C46A from helicobacter felis -

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Basic information

Entry
Database: PDB / ID: 3lwg
TitleCrystal structure of HP0420-homologue C46A from helicobacter felis
ComponentsHP0420 homologue
KeywordsUNKNOWN FUNCTION / Helicobacter / hotdog-fold / structural genomics
Function / homologyHotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / membrane / Alpha Beta / HP0420 homologue
Function and homology information
Biological speciesHelicobacter felis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHa, N.-C. / Piao, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystal structure and functional insight of HP0420-homolog from Helicobacter felis
Authors: Piao, S. / Jin, X.L. / Yun, B.-Y. / Kim, N. / Cho, H.-S. / Fukuda, M. / Lee, H. / Ha, N.-C.
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 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
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: HP0420 homologue
B: HP0420 homologue


Theoretical massNumber of molelcules
Total (without water)32,1332
Polymers32,1332
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-16 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.302, 67.129, 70.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HP0420 homologue


Mass: 16066.624 Da / Num. of mol.: 2 / Mutation: C46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter felis (bacteria) / Plasmid: pROEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5MNX9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION, AND THE NUCLEOTIDE SEQUENCE HAS BEEN SUBMITTED TO GENBANK. C46A IS A MUTATION IN THE SEQUENCE.

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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: 1.95 Å3/Da / Density % sol: 37.07 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 6.5
Details: 0.01M Cobalt(II)chloride hexahydrate, 0.1M MES pH6.5, 1.8M ammonium sulfate., EVAPORATION, temperature 287K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2009 / Details: Double mirror
RadiationMonochromator: Double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 23917 / Num. obs: 23847 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 30.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1165 / Rsym value: 0.318 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LW3

3lw3


Resolution: 1.8→48.52 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 49922.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2352 9.9 %RANDOM
Rwork0.1804 ---
all0.182 23977 --
obs0.182 23816 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9767 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2--2.38 Å20 Å2
3----1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.8→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 118 2128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d1.64
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2 390 10.3 %
Rwork0.186 3404 -
obs-2352 96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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