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- PDB-3q34: The crystal structure of YceI-like family protein from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 3q34
TitleThe crystal structure of YceI-like family protein from Pseudomonas syringae
ComponentsYceI-like family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Uncharacterised protein with YceI domain / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ubiquinone-8 / YceI-like family protein
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsZhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: TO BE PUBLISHED
Title: The crystal structure of YceI-like family protein from Pseudomonas syringae
Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID / _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

Downloads & links

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Assembly

Deposited unit
A: YceI-like family protein
B: YceI-like family protein
C: YceI-like family protein
D: YceI-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,19311
Polymers83,0084
Non-polymers3,1857
Water9,278515
1
A: YceI-like family protein
C: YceI-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0505
Polymers41,5042
Non-polymers1,5463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-5 kcal/mol
Surface area14330 Å2
MethodPISA
2
B: YceI-like family protein
D: YceI-like family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1436
Polymers41,5042
Non-polymers1,6384
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-2 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.647, 103.357, 63.193
Angle α, β, γ (deg.)90.00, 109.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
YceI-like family protein


Mass: 20752.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Strain: pv. phaseolicola / Gene: PSPPH_4050 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codon+RIL(p)-stratagene / References: UniProt: Q48EL2
#2: Chemical
ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H74O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→59.7 Å / Num. obs: 72488 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→47.481 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / σ(F): 2.59 / Phase error: 19.44 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 3656 5.05 %Random
Rwork0.1703 ---
obs0.1722 72447 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.459 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso mean: 17.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.8996 Å20 Å2-1.8152 Å2
2---0.859 Å20 Å2
3----1.0405 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5383 0 230 515 6128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145828
X-RAY DIFFRACTIONf_angle_d1.6977925
X-RAY DIFFRACTIONf_dihedral_angle_d19.3922299
X-RAY DIFFRACTIONf_chiral_restr0.117907
X-RAY DIFFRACTIONf_plane_restr0.0081004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72240.24611410.20892485X-RAY DIFFRACTION94
1.7224-1.7460.24851350.20452603X-RAY DIFFRACTION99
1.746-1.77090.25261340.18912661X-RAY DIFFRACTION100
1.7709-1.79730.25541460.18952614X-RAY DIFFRACTION100
1.7973-1.82540.21831420.17992659X-RAY DIFFRACTION100
1.8254-1.85540.21051480.17052653X-RAY DIFFRACTION100
1.8554-1.88740.22221560.17362626X-RAY DIFFRACTION100
1.8874-1.92170.20081430.17072633X-RAY DIFFRACTION100
1.9217-1.95860.23671480.16442659X-RAY DIFFRACTION100
1.9586-1.99860.21331510.16372611X-RAY DIFFRACTION100
1.9986-2.04210.2051390.15172686X-RAY DIFFRACTION100
2.0421-2.08960.20881270.15792659X-RAY DIFFRACTION100
2.0896-2.14180.23671470.15852629X-RAY DIFFRACTION100
2.1418-2.19970.22031370.16332686X-RAY DIFFRACTION100
2.1997-2.26450.21551580.16332607X-RAY DIFFRACTION100
2.2645-2.33760.21781230.17042690X-RAY DIFFRACTION100
2.3376-2.42110.22441280.16562665X-RAY DIFFRACTION100
2.4211-2.5180.22541250.17622680X-RAY DIFFRACTION100
2.518-2.63260.20711440.17752644X-RAY DIFFRACTION100
2.6326-2.77140.22471570.17662630X-RAY DIFFRACTION100
2.7714-2.9450.21831360.18372654X-RAY DIFFRACTION100
2.945-3.17240.19441270.17192680X-RAY DIFFRACTION100
3.1724-3.49150.18511380.15282647X-RAY DIFFRACTION100
3.4915-3.99650.16771510.14732661X-RAY DIFFRACTION100
3.9965-5.03430.16871540.14452650X-RAY DIFFRACTION99
5.0343-47.49920.19551210.19992719X-RAY DIFFRACTION99

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