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- PDB-1yk5: Pyrococcus abyssi rubredoxin -

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Basic information

Entry
Database: PDB / ID: 1yk5
TitlePyrococcus abyssi rubredoxin
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 ...Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsBonisch, H. / Schmidt, C.L. / Bianco, P. / Ladenstein, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.
Authors: Bonisch, H. / Schmidt, C.L. / Bianco, P. / Ladenstein, R.
History
DepositionJan 17, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rubredoxin
B: Rubredoxin
C: Rubredoxin
D: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4108
Polymers24,1874
Non-polymers2234
Water2,828157
1
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1032
Polymers6,0471
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1032
Polymers6,0471
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1032
Polymers6,0471
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1032
Polymers6,0471
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.301, 59.513, 80.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Rubredoxin / Rd


Mass: 6046.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: rub / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9V099
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: Ammonium sulfate, MES, Dioxane, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 2002
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→40.37 Å / Num. obs: 24841 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.7
Reflection shellResolution: 1.78→1.81 Å / Rsym value: 0.504 / % possible all: 89

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Processing

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

1brf


Resolution: 1.79→40.37 Å / Isotropic thermal model: Individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1266 5.1 %RANDOM
Rwork0.158 ---
obs0.158 24841 98.1 %-
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.79→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 4 157 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0191728
X-RAY DIFFRACTIONr_angle_refined_deg1.7122338
X-RAY DIFFRACTIONr_chiral_restr0.122223
X-RAY DIFFRACTIONr_gen_planes_refined0.0081949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.757207

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