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- PDB-4i66: Crystal structure of Hoch_4089 protein from Haliangium ochraceum -

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Basic information

Entry
Database: PDB / ID: 4i66
TitleCrystal structure of Hoch_4089 protein from Haliangium ochraceum
Componentsuncharacterized protein Hoch_4089
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyDomain of unknown function DUF4159 / Domain of unknown function DUF4159 / Domain of unknown function (DUF4159) / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DUF4159 domain-containing protein
Function and homology information
Biological speciesHaliangium ochraceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsMichalska, K. / Mack, J.C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Hoch_4089 protein from Haliangium ochraceum
Authors: Michalska, K. / Mack, J.C. / Endres, M. / Joachimiak, A.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: uncharacterized protein Hoch_4089
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5803
Polymers23,3881
Non-polymers1922
Water3,135174
1
A: uncharacterized protein Hoch_4089
hetero molecules

A: uncharacterized protein Hoch_4089
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1606
Polymers46,7762
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area1800 Å2
ΔGint-62 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.185, 58.185, 94.779
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

21A-301-

SO4

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Components

#1: Protein uncharacterized protein Hoch_4089


Mass: 23387.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (bacteria) / Strain: DSM 14365 / Gene: Hoch_4089 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: D0LJL3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Li2SO4, 0.1 M HEPES/NaOH pH 7.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 46523 / Num. obs: 46401 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 30.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2297 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
BUCCANEERmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→22.25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.584 / SU ML: 0.031 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19843 1177 2.5 %RANDOM
Rwork0.15897 ---
all0.15991 46401 --
obs0.15991 46401 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.766 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.3→22.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 10 174 1740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221633
X-RAY DIFFRACTIONr_bond_other_d0.0010.021149
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9932214
X-RAY DIFFRACTIONr_angle_other_deg0.93532762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04221.94877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85715264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7821520
X-RAY DIFFRACTIONr_chiral_restr0.0940.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
X-RAY DIFFRACTIONr_mcbond_it1.7931.51017
X-RAY DIFFRACTIONr_mcbond_other0.51.5411
X-RAY DIFFRACTIONr_mcangle_it2.86421626
X-RAY DIFFRACTIONr_scbond_it3.693616
X-RAY DIFFRACTIONr_scangle_it5.6414.5588
X-RAY DIFFRACTIONr_rigid_bond_restr1.47332782
LS refinement shellResolution: 1.299→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 81 -
Rwork0.213 3283 -
obs--99.73 %

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