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- PDB-2e2e: TPR domain of NrfG mediates the complex formation between heme ly... -

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Basic information

Entry
Database: PDB / ID: 2e2e
TitleTPR domain of NrfG mediates the complex formation between heme lyase and formate-dependent nitrite reductase in Escherichia Coli O157:H7
ComponentsFormate-dependent nitrite reductase complex nrfG subunit
KeywordsLYASE / TPR / cytochrome c biogenesis / O157:H7 EDL933 / NrfG / formate-dependent nitrite reductase complex
Function / homology
Function and homology information


: / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / IMIDAZOLE / Formate-dependent nitrite reductase complex subunit NrfG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsHan, D. / Kim, K. / Oh, J. / Park, J. / Kim, Y.
CitationJournal: Proteins / Year: 2008
Title: TPR domain of NrfG mediates complex formation between heme lyase and formate-dependent nitrite reductase in Escherichia coli O157:H7.
Authors: Han, D. / Kim, K. / Oh, J. / Park, J. / Kim, Y.
History
DepositionNov 11, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formate-dependent nitrite reductase complex nrfG subunit
B: Formate-dependent nitrite reductase complex nrfG subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5416
Polymers41,2462
Non-polymers2944
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.802, 85.824, 49.073
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 31 - 206 / Label seq-ID: 2 - 177

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
21BB
32AA
42BB

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Components

#1: Protein Formate-dependent nitrite reductase complex nrfG subunit


Mass: 20623.137 Da / Num. of mol.: 2 / Fragment: Tetratricopeptide repeat motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157 : H7 EDL933 / Gene: nrfG / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)codonplus Ril / References: UniProt: Q8X5S3
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.1 %

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Data collection

Diffraction
IDCrystal-ID
11
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.97950, 0.97956, 0.97171
SYNCHROTRONPAL/PLS 6B2
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMay 13, 2005
ADSC QUANTUM 2102CCDMay 13, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979561
30.971711
ReflectionResolution: 2.05→45 Å / Num. obs: 22119 / % possible obs: 98.65 %
Reflection shellResolution: 2.05→2.1 Å / % possible all: 95.65

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→45 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.697 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2450 10 %RANDOM
Rwork0.23126 ---
obs0.23499 22119 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.528 Å2
Baniso -1Baniso -2Baniso -3
1-5.07 Å20 Å2-0.01 Å2
2---1.97 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 18 190 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212884
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9293898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3955338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86424.512164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19915500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.861522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022236
X-RAY DIFFRACTIONr_nbd_refined0.2290.21402
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.220
X-RAY DIFFRACTIONr_mcbond_it0.7461.51750
X-RAY DIFFRACTIONr_mcangle_it1.20422714
X-RAY DIFFRACTIONr_scbond_it2.07131294
X-RAY DIFFRACTIONr_scangle_it3.1414.51184
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2812 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.010.05
tight thermal0.050.5
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 155 -
Rwork0.252 1603 -
obs--95.65 %
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)
11.92092.49580.7053.92420.82212.4389-0.13530.1820.245-0.35540.20840.15660.38850.0833-0.0731-0.10260.0256-0.0301-0.09450.0371-0.059611.622222.529330.0725
21.79312.3825-0.68543.7857-0.8412.4967-0.16410.1929-0.2498-0.36550.2294-0.1502-0.3859-0.0817-0.0653-0.10960.01980.0363-0.0959-0.0352-0.052312.29484.97095.5416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA31 - 502 - 21
2X-RAY DIFFRACTION1AA56 - 20627 - 177
3X-RAY DIFFRACTION2BB31 - 502 - 21
4X-RAY DIFFRACTION2BB56 - 20627 - 177

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