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- PDB-4rgk: Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Pr... -

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Basic information

Entry
Database: PDB / ID: 4rgk
TitleCrystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Chicago Center for Functional Annotation / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta fold / beta-barrel
Function / homology
Function and homology information


Gig2-like / Gig2-like / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DUF1479 domain-containing protein / DUF1479 domain-containing protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Joachimiak, A.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Oct 9, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9867
Polymers47,5161
Non-polymers4706
Water2,936163
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,97314
Polymers95,0322
Non-polymers94112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5400 Å2
ΔGint-54 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.750, 54.659, 93.152
Angle α, β, γ (deg.)90.00, 124.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-747-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 47516.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: y1506, YPO2976, YP_2601 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 gold / References: UniProt: Q7CJE8, UniProt: A0A2U2H2N4*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2 M lithium sulfate, 0.1 M CAPS pH 10.5, 1.2M monosodium dihydrogen phosphate/0.8 M dipotasium monohydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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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: Dec 16, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochormator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 25801 / Num. obs: 25801 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.07 Å2 / Rsym value: 0.127 / Net I/σ(I): 9.06
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.13 / Num. unique all: 1135 / Rsym value: 0.471 / % possible all: 88.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→47.711 Å / SU ML: 0.25 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1252 5.14 %random
Rwork0.191 ---
all0.194 24360 --
obs0.194 24360 92.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.89 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 28 163 3501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093497
X-RAY DIFFRACTIONf_angle_d1.1494754
X-RAY DIFFRACTIONf_dihedral_angle_d16.3441304
X-RAY DIFFRACTIONf_chiral_restr0.048495
X-RAY DIFFRACTIONf_plane_restr0.006643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.15-2.23390.2828950.2251831192667
2.2339-2.33550.29331140.21512183229779
2.3355-2.45870.28841420.21592467260989
2.4587-2.61270.22831650.21072643280897
2.6127-2.81440.25541560.207427712927100
2.8144-3.09760.29831530.210527542908100
3.0976-3.54570.23211360.18528242959100
3.5457-4.46670.20821380.16432787292599
4.4667-47.72290.21721530.17932848300199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.96460.4073-0.32291.9489-0.93532.028-0.0544-0.0083-0.0997-0.15490.01720.05850.213-0.16950.03310.09910.0618-0.01260.1279-0.03190.1654-8.5812-3.441258.5792
22.33180.6973-0.06872.866-1.56675.50520.4043-1.2005-0.94830.4336-0.3715-0.66220.66090.9296-0.0480.5226-0.0014-0.15290.65310.19760.853218.460215.404758.0469
30.35860.3535-0.47452.0366-0.9452.12890.0181-0.05810.07720.0941-0.0461-0.0078-0.08030.03560.02250.13660.0014-0.020.1758-0.02680.1848-6.10743.513960.1704
43.69822.5139-1.04742.8361-0.18393.82260.0910.00620.548-0.0352-0.11430.3337-0.413-0.03320.00660.29770.0294-0.01920.1503-0.00620.2524-1.979523.588451.8191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 379 )
4X-RAY DIFFRACTION4chain 'A' and (resid 380 through 415 )

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