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- PDB-4fz4: Crystal structure of HP0197-18kd -

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Basic information

Entry
Database: PDB / ID: 4fz4
TitleCrystal structure of HP0197-18kd
ComponentsUncharacterized protein conserved in bacteria
KeywordsIMMUNE SYSTEM / surface antigen
Function / homologyButyryl-CoA Dehydrogenase, subunit A; domain 3 - #130 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha / NITRATE ION / :
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44 Å
AuthorsYuan, Z. / Yan, X.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Molecular mechanism by which surface antigen HP0197 mediates host cell attachment in the pathogenic bacteria Streptococcus suis
Authors: Yuan, Z.Z. / Yan, X.J. / Zhang, A.D. / Chen, B. / Shen, Y.Q. / Jin, M.L.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
A: Uncharacterized protein conserved in bacteria
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1574
Polymers18,0241
Non-polymers1333
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.235, 87.601, 38.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

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Components

#1: Protein Uncharacterized protein conserved in bacteria / 0197-18kd


Mass: 18024.191 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 51-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 98HAH33 / Gene: SSU98_0197 / Production host: Escherichia coli (E. coli) / References: UniProt: A4VZ16
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 30% PEG 3350, 0.4M NaNO3 , pH 7.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Nov 20, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. all: 7687 / Num. obs: 6551 / % possible obs: 85.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.44→18.82 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 850665.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 336 5.1 %RANDOM
Rwork0.222 ---
all0.263 7687 --
obs0.222 6551 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.4455 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 47.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2--4.73 Å20 Å2
3----3.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.44→18.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 6 31 1304
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it5.721.5
X-RAY DIFFRACTIONc_mcangle_it8.082
X-RAY DIFFRACTIONc_scbond_it8.462
X-RAY DIFFRACTIONc_scangle_it11.742.5
LS refinement shellResolution: 2.44→2.59 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 56 5.3 %
Rwork0.273 993 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4no3.paramno3.top

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