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- PDB-3lw3: Crystal structure of HP0420-homologue from Helicobacter felis -

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Basic information

Entry
Database: PDB / ID: 3lw3
TitleCrystal structure of HP0420-homologue 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: 1.6 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HP0420 homologue
B: HP0420 homologue


Theoretical massNumber of molelcules
Total (without water)32,1972
Polymers32,1972
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-20 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.559, 70.341, 53.860
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: 16098.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter felis (bacteria) / Plasmid: pPROEX-HTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5MNX8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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.

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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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 2.0M 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: Jun 18, 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: 1.6→30 Å / Num. all: 36102 / Num. obs: 35413 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 49.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2992 / Rsym value: 0.4 / % possible all: 84.6

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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 3BNV

3bnv


Resolution: 1.6→29.51 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 516369.58 / 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
Rfree0.266 2506 7.1 %RANDOM
Rwork0.208 ---
all0.2102 36008 --
obs0.2102 35375 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.446 Å2 / ksol: 0.65 e/Å3
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å20 Å20 Å2
2--5.06 Å20 Å2
3----1.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.6→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 0 173 2150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.386 5294 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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