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- PDB-7te5: Crystal Structure of the Pirin Family Protein Redox-sensitive Bic... -

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Basic information

Entry
Database: PDB / ID: 7te5
TitleCrystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK from Yersinia pestis
ComponentsPirin family protein Yhak
KeywordsMETAL BINDING PROTEIN / pirin family protein / bicupin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / Pirin, C-terminal domain / Pirin C-terminal cupin domain / Pirin, N-terminal domain / Pirin / Pirin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls ...: / Pirin, C-terminal domain / Pirin C-terminal cupin domain / Pirin, N-terminal domain / Pirin / Pirin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
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 Pirin Family Protein Redox-sensitive Bicupin YhaK from Yersinia pestis
Authors: Kim, Y. / Chhor, G. / Endres, M. / Babnigg, G. / Schneewind, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pirin family protein Yhak
B: Pirin family protein Yhak
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3344
Polymers64,2862
Non-polymers492
Water7,116395
1
A: Pirin family protein Yhak
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1672
Polymers32,1431
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pirin family protein Yhak
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1672
Polymers32,1431
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.442, 66.442, 122.546
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein Pirin family protein Yhak / Pirin-related protein


Mass: 32142.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: YP_1950, EGX46_10965 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A2U2H063
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M tri-sodium citrate pH 5.6, 10 %(w/v) PEG4000, 10 %(w/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 50165 / % possible obs: 97.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.553 / Num. unique obs: 1995 / CC1/2: 0.589 / % possible all: 77.6

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
SBC-Collectdata collection
HKL-3000data scaling
HKL-3000data processing
HKL-3000phasing
MLPHAREphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→33.31 Å / Cross valid method: FREE R-VALUE / σ(F): 2.28 / Phase error: 21.5908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 2460 4.92 %
Rwork0.1668 47525 -
obs0.1747 49985 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.79 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 2 395 4757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434537
X-RAY DIFFRACTIONf_angle_d0.73376180
X-RAY DIFFRACTIONf_chiral_restr0.0498659
X-RAY DIFFRACTIONf_plane_restr0.005828
X-RAY DIFFRACTIONf_dihedral_angle_d5.9982620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.25251260.24942175X-RAY DIFFRACTION72.16
1.89-1.930.21771240.24992514X-RAY DIFFRACTION82.72
1.93-1.980.2421260.23032714X-RAY DIFFRACTION89.51
1.98-2.030.24891550.21732780X-RAY DIFFRACTION92.21
2.03-2.080.25341340.21362907X-RAY DIFFRACTION95.22
2.08-2.140.21571250.21182899X-RAY DIFFRACTION95.83
2.14-2.210.20581280.20942915X-RAY DIFFRACTION95.79
2.21-2.290.23811360.2082863X-RAY DIFFRACTION95.47
2.29-2.380.26211340.2132903X-RAY DIFFRACTION95.56
2.38-2.490.27541480.21242844X-RAY DIFFRACTION95.05
2.49-2.620.23681720.20782866X-RAY DIFFRACTION94.34
2.62-2.780.21161080.20242935X-RAY DIFFRACTION96.45
2.79-30.21451690.18312833X-RAY DIFFRACTION94.31
3-3.30.19971460.16512899X-RAY DIFFRACTION95.17
3.3-3.780.2011460.1432858X-RAY DIFFRACTION95.14
3.78-4.760.17621660.12392882X-RAY DIFFRACTION94.34
4.76-33.310.21971660.14162789X-RAY DIFFRACTION92.66
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)
10.5826101161780.207851521195-0.3309611419180.645145062855-0.4096655968032.222446394440.004726554158550.103310832911-0.0567127879076-0.290543674125-0.0945747773123-0.1719908379950.06220176357050.143968767290.05257502292890.3359336191040.04813248803960.04563643535350.2481256882660.006292815631490.13545398364135.612191870627.68452986226.2249966644
20.55554095850.715535830619-0.5171459511471.28600572937-1.262729055521.45484490680.0793588733292-0.121265707618-0.0134174339510.239892422994-0.119524750741-0.0678504718717-0.2618484668110.0154542223640.0251806969520.3516831096550.04642859576870.02645903868680.23235219255-0.00246273952830.14740241613334.094251871130.901166217842.8457567277
34.247800193060.4716539634130.2365203094591.95095879769-0.05589624071290.4147163354280.0464104082302-0.0579350466650.01750519285050.140889263861-0.07837335251690.165012358155-0.245644023117-0.06820515046660.02323627854720.3521869245590.07239704658260.06101597330240.21408746956-0.008718004611440.14972374813726.463611425243.257693255132.9783134688
42.146686412140.5206910285090.3508189674171.897186198740.2645024967660.499710357425-0.00790344195847-0.04723242396690.0099523047032-0.0792232620928-0.1016876827360.0608072624894-0.0846823822164-0.06761916767560.09854916355020.2697523787940.02266369383210.04168416362220.244220633496-0.005047497093220.063902719108333.148075663835.718242001123.9052011217
50.65394985217-0.4903670628870.2351953804961.15139892834-0.721563820220.42395231889-0.0652136410669-0.13518592445-0.0563484414282-0.04678245134620.0746361264640.06152820863610.1120263210330.1159444099430.01783979177120.3062997843720.0319381694878-0.01090725096540.2555580493620.02607915943590.14580069917756.44537337892.0178368871442.6998898696
61.96346347827-0.0442592746593-1.479290426770.8477226871070.3557870949031.293682993020.04157661305340.3188448030950.0148915372303-0.171380365296-0.04442560094390.0329212033520.0110717012433-0.08849223554490.01339747585530.2564627055520.0685099912378-0.01345649837360.2765384781480.02414344430940.11764778383154.50166568784.7340667887725.0595186813
72.35027714236-0.05718439407550.6460910679970.718167316526-0.3890359714270.7560836224120.01681573571740.05890476473610.170779224139-0.00378757713613-0.0557147408502-0.0927510590999-0.08051466092480.03714227215610.03554445244990.3428224311020.06387451804570.02650416047070.2158221653130.02154850846440.14044638370755.910173349917.554754717240.7072972396
81.608690337850.375273051423-0.7430618791891.827394911620.1770039792450.724566338432-0.0661799450316-0.0279003355116-0.08674285333940.0732294354248-0.1087807465410.209100569003-0.00343741492695-0.1285581792770.1511852744050.2603434654220.05720258783570.01375421023060.2113448084390.03535976363850.14965133144846.17821108742.6193730863738.2690087257
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 49 )AA0 - 491 - 50
22chain 'A' and (resid 50 through 128 )AA50 - 12851 - 129
33chain 'A' and (resid 129 through 179 )AA129 - 179130 - 180
44chain 'A' and (resid 180 through 283 )AA180 - 283181 - 284
55chain 'B' and (resid 0 through 37 )BC0 - 371 - 38
66chain 'B' and (resid 38 through 138 )BC38 - 13839 - 139
77chain 'B' and (resid 139 through 228 )BC139 - 228140 - 229
88chain 'B' and (resid 229 through 283 )BC229 - 283230 - 284

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