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- PDB-7twc: Crystal Structure of the Putative Oxidoreductase of DUF1479-conta... -

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Basic information

Entry
Database: PDB / ID: 7twc
TitleCrystal Structure of the Putative Oxidoreductase of DUF1479-containing Protein Family YPO2976 from Yersinia pestis Bound to CAPS
ComponentsDUF1479 domain-containing protein
KeywordsUNKNOWN FUNCTION / Uncharacterized protein / oxidoreductase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyGig2-like / Gig2-like / Isopenicillin N synthase-like superfamily / PHOSPHATE ION / DUF1479 domain-containing protein
Function and homology information
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Putative Oxidoreductase of DUF1479-containing Protein Family YPO2976 from Yersinia pestis Bound to CAPS
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF1479 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,61012
Polymers47,5161
Non-polymers1,09411
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.964, 54.699, 93.163
Angle α, β, γ (deg.)90.000, 124.172, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DUF1479 domain-containing protein


Mass: 47516.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: YPO2976 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: A0A3G5LE49

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Non-polymers , 6 types, 320 molecules

#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH pH 10.5, 1.2 M Sodium-Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 41213 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.18 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.039 / Rrim(I) all: 0.076 / Net I/σ(I): 16.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 1940 / CC1/2: 0.681 / Rpim(I) all: 0.469 / Rrim(I) all: 0.796 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→24.14 Å / SU ML: 0.1904 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194 2003 5.04 %
Rwork0.1555 37717 -
obs0.1575 39720 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.82 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 63 309 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01223584
X-RAY DIFFRACTIONf_angle_d1.10754882
X-RAY DIFFRACTIONf_chiral_restr0.072506
X-RAY DIFFRACTIONf_plane_restr0.0123654
X-RAY DIFFRACTIONf_dihedral_angle_d14.80691336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.2866760.25851779X-RAY DIFFRACTION62.12
1.89-1.940.28061300.21892355X-RAY DIFFRACTION83.81
1.94-20.23081250.17712608X-RAY DIFFRACTION92.55
2-2.070.19411340.172742X-RAY DIFFRACTION98.06
2.07-2.140.25011530.162780X-RAY DIFFRACTION99.46
2.14-2.230.19591400.16092828X-RAY DIFFRACTION99.8
2.23-2.330.21441460.15962804X-RAY DIFFRACTION99.86
2.33-2.450.20881640.15442808X-RAY DIFFRACTION99.9
2.45-2.60.20681730.15022775X-RAY DIFFRACTION99.93
2.6-2.80.18121550.15332823X-RAY DIFFRACTION99.97
2.8-3.080.18251550.15562828X-RAY DIFFRACTION99.97
3.08-3.530.18941460.14082834X-RAY DIFFRACTION100
3.53-4.440.14861480.13242848X-RAY DIFFRACTION99.73
4.44-24.140.19621580.16012905X-RAY DIFFRACTION99.16
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)
14.56461231323-3.71416846954-0.200328963525.67991126451-0.2018082490581.886952694220.140727437140.4555656106950.203285488155-0.385048978887-0.219917380712-0.15223674014-0.0781832346144-0.007412409071290.04431231711110.249966729321-0.01041892840090.0001609046608530.2240342456780.0279528730070.13707799139212.453973589-0.362791313805-7.83734776415
20.6762217851670.0440244673517-0.008920721162530.852200391675-0.3610279971111.96591844592-0.0113036922668-0.0586928048436-0.1106337552030.1610816556870.00937136447818-0.1151066211830.5827795064370.114805997631-0.0385649845460.1521171619880.0355862525923-0.0144955550550.1156681170580.01946901557790.15141923957917.3939205199-14.201305986220.1039211773
30.4235537898-0.501955730893-0.4160561861341.608934590450.2418659302311.28474463854-0.01061328248570.0539581457873-0.0265347001287-0.013804275608-0.03825412212610.0385306683687-0.0705659043751-0.03195685623030.01827940736750.0863843685269-0.0368317582244-0.02372131140590.113844720573-0.01597065535870.09933419608499.292222883388.5034652411526.1428192196
40.392003529679-0.156404097869-0.2709610190340.9307534938130.5012814307711.477499185770.007883204452040.0261870481130.0300180372762-0.0743505900499-0.02900799390160.03697228185790.0255835179384-0.02701879007590.02491094933730.0834477329246-0.0020920360099-0.01411160075980.09920775837950.01288018121870.1094028311489.46385948932-0.0048490970055114.741109948
52.74590496464-1.10739969541-0.4082581511352.154548200580.439382815354.044491956810.03187239586920.004422693914240.2892972688670.02246002152210.0104155100199-0.161062166093-0.2951144549890.0286583914649-0.006418455373830.148900060657-0.0165216698566-0.01120219600310.03548133806330.01145539991670.1372363266287.5120293481722.242398400925.3848730795
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 27 )0 - 271 - 28
22chain 'A' and (resid 28 through 71 )28 - 7129 - 72
33chain 'A' and (resid 72 through 182 )72 - 18273 - 183
44chain 'A' and (resid 183 through 379 )183 - 379184 - 380
55chain 'A' and (resid 380 through 415 )380 - 415381 - 416

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