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- PDB-5tf3: Crystal Structure of Protein of Unknown Function YPO2564 from Yer... -

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Basic information

Entry
Database: PDB / ID: 5tf3
TitleCrystal Structure of Protein of Unknown Function YPO2564 from Yersinia pestis
ComponentsPutative membrane protein
KeywordsOXIDOREDUCTASE / alpha structure / Functional Genomics / Chicago Center for Functional Annotation / CCFA / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyProtein of unknown function DUF1198 / Protein of unknown function (DUF1198) / Putative membrane protein / Putative membrane protein
Function and homology information
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Anderson, W.F. / Crosson, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of Protein of Unknown Function YPO2564 from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Anderson, W.F. / Crosson, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references / Structure summary
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3202
Polymers15,2581
Non-polymers621
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.094, 75.094, 73.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative membrane protein


Mass: 15257.792 Da / Num. of mol.: 1 / Fragment: UNP residues 22-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: A0A0H2W5S9, UniProt: A0A2U2GWH2*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.97 Å3/Da / Density % sol: 69.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5, 20%(w/v) PEG8000

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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: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16095 / % possible obs: 96.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 34.74 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 19.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.577 / % possible all: 78.7

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Processing

Software
NameVersionClassification
PHENIXdev_2411refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.001→33.462 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 862 5.36 %random
Rwork0.1984 ---
obs0.1996 16072 96.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.4 Å2
Refinement stepCycle: LAST / Resolution: 2.001→33.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1066 0 4 61 1131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071180
X-RAY DIFFRACTIONf_angle_d0.8211607
X-RAY DIFFRACTIONf_dihedral_angle_d18.89720
X-RAY DIFFRACTIONf_chiral_restr0.046173
X-RAY DIFFRACTIONf_plane_restr0.006214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0011-2.12650.3251280.27542163X-RAY DIFFRACTION84
2.1265-2.29060.2681220.23592561X-RAY DIFFRACTION98
2.2906-2.52110.27431430.21072598X-RAY DIFFRACTION100
2.5211-2.88570.26051490.21422610X-RAY DIFFRACTION100
2.8857-3.6350.22371640.20152614X-RAY DIFFRACTION100
3.635-33.46690.17691560.17332664X-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)
14.11373.67450.04545.6763-0.41910.88260.2190.4991-0.52580.14630.2004-1.0145-0.29750.3134-0.26680.3071-0.1066-0.00060.3108-0.00450.3468-13.026725.4443-5.1896
23.35011.34920.45965.3542.57482.55070.3648-0.36070.27880.4141-0.2028-0.3149-0.3990.3969-0.13940.4556-0.14510.06670.3576-0.0080.2877-18.021130.5397-0.5231
34.73580.1299-0.54193.78850.37082.87470.498-0.81270.02910.4783-0.4037-0.0159-0.1650.36190.01040.3271-0.14730.00490.3543-0.01960.2649-26.100323.67822.3714
44.0178-2.1029-0.67165.4953-0.60753.83220.17770.2162-0.34510.0461-0.340.25590.2754-0.39850.04680.2696-0.0749-0.0320.2161-0.05250.3124-31.872716.3391-2.927
52.03510.7895-0.35872.26150.76992.55390.8284-1.00590.36370.9782-0.45750.187-0.58110.9506-0.07350.7413-0.48720.17390.6052-0.11570.4077-26.743527.44138.1778
60.8038-0.32290.09391.62250.05650.35980.1356-0.23660.0321-0.09010.17180.4244-0.11270.14980.24230.1672-0.60250.30660.1551-0.11380.4275-37.625422.458110.0085
78.75391.5079-9.12110.3599-1.55539.5065-0.3881-0.7992-0.99020.95360.1654-0.03040.9395-0.37580.01530.6247-0.1260.1320.5884-0.10660.806-34.92286.42758.3017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 140 )
7X-RAY DIFFRACTION7chain 'A' and (resid 141 through 149 )

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