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- PDB-1r7h: NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapp... -

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Basic information

Entry
Database: PDB / ID: 1r7h
TitleNrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer
ComponentsNrdH-redoxin
KeywordsELECTRON TRANSPORT / NRDH / THIOREDOXIN / GLUTAREDOXIN / REDOX PROTEIN / DOMAIN SWAPPING
Function / homology
Function and homology information


cell redox homeostasis / electron transfer activity
Similarity search - Function
Glutaredoxin-like protein NrdH / : / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin-like protein NrdH
Similarity search - Component
Biological speciesCorynebacterium ammoniagenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsStehr, M. / Lindqvist, Y.
CitationJournal: Proteins / Year: 2004
Title: NrdH-redoxin of Corynebacterium ammoniagenes forms a domain-swapped dimer.
Authors: Stehr, M. / Lindqvist, Y.
History
DepositionOct 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NrdH-redoxin
B: NrdH-redoxin


Theoretical massNumber of molelcules
Total (without water)16,5992
Polymers16,5992
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-32 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.63, 89.63, 40.15
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
12A
22B
32A
42B
52A
62B
72A
82B

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETVALVALAA1 - 121 - 12
211METMETVALVALBB1 - 121 - 12
321CYSCYSASPASPAA14 - 2214 - 22
421CYSCYSASPASPBB14 - 2214 - 22
531ALAALATYRTYRAA24 - 2824 - 28
631ALAALATYRTYRBB24 - 2824 - 28
741THRTHRVALVALAA30 - 3130 - 31
841THRTHRVALVALBB30 - 3130 - 31
951ILEILEASPASPAA33 - 3633 - 36
1051ILEILEASPASPBB33 - 3633 - 36
1161ALAALAALAALAAA3939
1261ALAALAALAALABB3939
1371TYRTYRVALVALAA42 - 4342 - 43
1471TYRTYRVALVALBB42 - 4342 - 43
1581ALAALATYRTYRAA45 - 4845 - 48
1681ALAALATYRTYRBB45 - 4845 - 48
112GLNGLNVALVALAA50 - 5450 - 54
212GLNGLNVALVALBB50 - 5450 - 54
322VALVALGLUGLUAA56 - 5956 - 59
422VALVALGLUGLUBB56 - 5956 - 59
532TRPTRPILEILEAA61 - 6961 - 69
632TRPTRPILEILEBB61 - 6961 - 69
742GLNGLNGLNGLNAA71 - 7371 - 73
842GLNGLNGLNGLNBB71 - 7371 - 73

NCS ensembles :
ID
1
2

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Components

#1: Protein NrdH-redoxin


Mass: 8299.427 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium ammoniagenes (bacteria)
Gene: nrdh / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O69271
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.86
Details: Na-citrate, Tris, MPD, spermidine, pH 7.86, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.69→25 Å / Num. all: 5187 / Num. obs: 5187 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.69→2.76 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H75

1h75


Resolution: 2.69→23.7 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.856 / SU B: 13.925 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.652 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 237 4.6 %RANDOM
Rwork0.24305 ---
all0.24787 5179 --
obs0.24513 4942 98.31 %-
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: 30.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å20 Å2
2--0.55 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.69→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1150 0 0 37 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221172
X-RAY DIFFRACTIONr_bond_other_d0.0010.021064
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.9591592
X-RAY DIFFRACTIONr_angle_other_deg0.69432472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1485146
X-RAY DIFFRACTIONr_chiral_restr0.0520.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
X-RAY DIFFRACTIONr_nbd_refined0.1510.2211
X-RAY DIFFRACTIONr_nbd_other0.1910.21165
X-RAY DIFFRACTIONr_nbtor_other0.0830.2659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.218
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.080.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.23
X-RAY DIFFRACTIONr_mcbond_it0.3111.5736
X-RAY DIFFRACTIONr_mcangle_it0.57621184
X-RAY DIFFRACTIONr_scbond_it0.5233436
X-RAY DIFFRACTIONr_scangle_it0.9454.5408
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1561tight positional0.020.05
2327tight positional0.020.05
1561tight thermal0.182
2327tight thermal0.152
LS refinement shellResolution: 2.689→2.759 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.422 16
Rwork0.324 346

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