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

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Basic information

Entry
Database: PDB / ID: 7tfq
TitleCrystal Structure of the Pirin Family Protein Redox-sensitive Bicupin YhaK Bound to Copper Ion 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
COPPER (II) ION / FORMIC ACID / SUCCINIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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 Bound to Copper Ion 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 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: Pirin family protein Yhak
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5417
Polymers32,1431
Non-polymers3986
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.133, 100.737, 45.498
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

21A-564-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 32142.791 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 187 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris Propane pH 7, 35 %(w/v) tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 30621 / % possible obs: 95.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.52 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1528 / CC1/2: 0.894 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→33.76 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.8937
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1956 1531 5.04 %
Rwork0.1655 28850 -
obs0.167 30381 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.81 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 23 181 2384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862341
X-RAY DIFFRACTIONf_angle_d1.04243186
X-RAY DIFFRACTIONf_chiral_restr0.0683336
X-RAY DIFFRACTIONf_plane_restr0.0082429
X-RAY DIFFRACTIONf_dihedral_angle_d14.4228855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.30341250.23332278X-RAY DIFFRACTION83.09
1.8-1.870.23581470.20392588X-RAY DIFFRACTION95.1
1.87-1.940.20711320.18482657X-RAY DIFFRACTION97.01
1.94-2.030.17781340.16532645X-RAY DIFFRACTION96.29
2.03-2.130.18541230.15582651X-RAY DIFFRACTION96.25
2.14-2.270.16321500.15512619X-RAY DIFFRACTION95.32
2.27-2.440.22231500.16652593X-RAY DIFFRACTION94.65
2.44-2.690.19661410.17152594X-RAY DIFFRACTION92.52
2.69-3.080.21051320.17522583X-RAY DIFFRACTION92.73
3.08-3.880.17891460.15582706X-RAY DIFFRACTION96.16
3.88-33.760.18931510.15462936X-RAY DIFFRACTION98.78
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)
13.36115190545-2.593207187530.8808517528694.03151026021-0.387467481410.6159509952480.1521760718470.0836231938383-0.5081379800820.0137531443008-0.1390621222080.3959020104030.1293053449140.00574483737130.01504091998240.153657526047-0.0168842367910.02779536755610.1468265103220.05214993722080.188794744535-4.2401941623813.340253856318.5535372595
21.15678533551-0.6103869315260.4447212436370.332974052587-0.06844141947022.163461541330.03915185654140.02360238487940.0505677508885-0.0334941171192-0.01702859787090.0375234032519-0.134639396011-0.0819951783683-0.02169147122120.114116690724-0.0118451597666-0.001045727938780.1208754958590.009331140741070.127829308964-2.0768689047930.033218722519.2943573208
31.96999142473-0.900393035099-1.422274169552.478227463850.5637462074772.387839253410.08786139898610.0767686526740.110880295891-0.1259202383740.0686796777354-0.229017294441-0.160983929379-0.0850524526566-0.0937584338150.0679194914386-0.0631911965793-0.006363819481830.120588250938-0.005434921154610.1604183392811.206896187229.755290714322.8666786484
41.090803497290.0995248534883-0.02124669390521.595974374240.6167223298051.51043705671-0.04025848676260.0796208899968-0.166083711702-0.0784368744860.104995933423-0.04358693180030.1199919029870.0270417245263-0.0619470060980.110466387511-0.00167243996738-0.004745419262940.1125080582230.001182550636120.1451689258619.2189731388713.203498622915.4329539396
52.87629780865-4.07522775188-0.1455072993186.2615516676-0.842666907753.92199370039-0.0900513724727-0.2212905884330.1430269995760.2131605672630.118984422179-0.0700904854493-0.01875202508580.0774020781766-0.02864983702370.095747553059-0.00403204016816-0.002057289859380.125258919179-0.007071170104160.0948613134509-3.901310497330.115043955339.9806275604
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 19 )0 - 191 - 20
22chain 'A' and (resid 20 through 128 )20 - 12821 - 129
33chain 'A' and (resid 129 through 152 )129 - 152130 - 153
44chain 'A' and (resid 153 through 257 )153 - 257154 - 258
55chain 'A' and (resid 258 through 283 )258 - 283259 - 284

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