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- PDB-5v4f: Crystal Structure of the Protein of Unknown Function of the Conse... -

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Basic information

Entry
Database: PDB / ID: 5v4f
TitleCrystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfB from Yersinia pestis
ComponentsPutative translational inhibitor protein
KeywordsStructural genomics / unknown function / alpha-beta fold / enamine/imine demainase (Rid) / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyYjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / Translational inhibitor protein / Translational inhibitor protein
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Krishnan, A. / Babnigg, G. / Schneewind, O. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: To Be Published
Title: Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfB from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Krishnan, A. / Babnigg, G. / Schneewind, O. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative translational inhibitor protein
B: Putative translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,31414
Polymers29,2082
Non-polymers1,10512
Water77543
1
A: Putative translational inhibitor protein
hetero molecules

A: Putative translational inhibitor protein
hetero molecules

A: Putative translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,47021
Polymers43,8133
Non-polymers1,65818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Buried area12190 Å2
ΔGint-54 kcal/mol
Surface area13560 Å2
MethodPISA
2
B: Putative translational inhibitor protein
hetero molecules

B: Putative translational inhibitor protein
hetero molecules

B: Putative translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,47021
Polymers43,8133
Non-polymers1,65818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area12000 Å2
ΔGint-54 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.205, 129.205, 129.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Putative translational inhibitor protein


Mass: 14604.212 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: tdcF4, y3550, YP_2945, YPO0628 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: Q7CGF8, UniProt: A0A380PLV4*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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 % sol: 80.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5, 30 5(w/v) PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14594 / % possible obs: 99.3 % / Redundancy: 4.8 % / Rsym value: 0.128 / Net I/σ(I): 10.1
Reflection shellResolution: 3→3.03 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 740 / CC1/2: 0.669 / Rsym value: 0.725 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2411)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 3.001→40.858 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.93
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 715 4.97 %random
Rwork0.1555 ---
obs0.1576 14380 97.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.4 Å2
Refinement stepCycle: LAST / Resolution: 3.001→40.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 72 43 2109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012128
X-RAY DIFFRACTIONf_angle_d1.0942888
X-RAY DIFFRACTIONf_dihedral_angle_d17.5851260
X-RAY DIFFRACTIONf_chiral_restr0.06330
X-RAY DIFFRACTIONf_plane_restr0.008378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0007-3.23230.2751360.21252616X-RAY DIFFRACTION94
3.2323-3.55740.22041340.18062723X-RAY DIFFRACTION99
3.5574-4.07180.21691750.13972725X-RAY DIFFRACTION100
4.0718-5.12840.14551170.12462796X-RAY DIFFRACTION100
5.1284-40.8620.19671530.16392805X-RAY DIFFRACTION97
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)
15.73133.0775-2.89056.7229-3.66539.33330.06570.34160.84550.06120.23780.6429-0.5638-0.6484-0.26420.46820.0581-0.06760.45820.01090.5664103.070933.949277.6229
21.848-0.29730.28612.12260.00032.1082-0.02140.16-0.007-0.0880.0230.08490.1009-0.01210.01730.37870.0005-0.02760.3693-0.0080.4177100.925615.516174.5585
39.9525-3.3362-2.31196.83873.09995.5635-0.2246-0.4-0.96710.55410.0371-0.05560.79110.39410.14740.54350.0059-0.07610.40320.02710.467784.456-2.170257.8521
41.8503-0.0160.47942.633-0.08461.6091-0.0662-0.04780.1497-0.04520.0375-0.13580.0330.09230.03540.43480.0164-0.02240.3844-0.00440.38886.7216.637360.6921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 133 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 28 )
4X-RAY DIFFRACTION4chain 'B' and (resid 29 through 133 )

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