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- PDB-9zdh: Crystal structure of rubredoxin from piezophilic hyperthermophili... -

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Basic information

Entry
Database: PDB / ID: 9zdh
TitleCrystal structure of rubredoxin from piezophilic hyperthermophilic archaeon Pyrococcus yayanosii
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / electron transfer / piezophilic / hyperthermophilic / archae
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. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
Biological speciesPyrococcus yayanosii CH1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsDoukov, T.I. / Rumley, M. / Jenney, F.E. / Cramer, S.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 2149122 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM65440 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
CitationJournal: Biomolecules / Year: 2026
Title: Crystallography of Extremophile Proteins-Structural Comparisons of Psychrophilic and Hyperthermophilic Rubredoxins
Authors: Doukov, T. / Turpin, T.F. / George, D. / Cole, C. / Drumright, K. / Rumley, M. / Boyce, R. / Jenney, F.E. / Cramer, S.P.
History
DepositionNov 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2477
Polymers18,0563
Non-polymers1914
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.914, 63.513, 78.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13B
23C

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 2 - 53 / Label seq-ID: 2 - 53

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
211BB
122AA
222CC
133BB
233CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Rubredoxin


Mass: 6018.755 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus yayanosii CH1 (archaea) / Gene: PYCH_09790 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8AEI5
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.9 Å3/Da / Density % sol: 35.38 % / Description: thin plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: VAPOR DIFFUSION AGAINST 3.2M NA,K PHOSPHATE, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.357→33.276 Å / Num. obs: 17219 / % possible obs: 89.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 20.31 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.447 / Rpim(I) all: 0.138 / Net I/σ(I): 6.4
Reflection shellResolution: 1.357→1.5 Å / Redundancy: 9.8 % / Rmerge(I) obs: 3.708 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 861 / CC1/2: 0.837 / Rpim(I) all: 1.216 / % possible all: 57.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.36→33.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.4 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.106
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.213 869 5.047 %
Rwork0.172 --
obs-17219 57.8 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.033 Å20 Å20 Å2
2--0.343 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.36→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 4 203 1440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121320
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161166
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.8511797
X-RAY DIFFRACTIONr_angle_other_deg0.5651.8022730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.21554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16910214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02260
X-RAY DIFFRACTIONr_nbd_refined0.2390.2258
X-RAY DIFFRACTIONr_nbd_other0.1560.290
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2632
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3981.545634
X-RAY DIFFRACTIONr_mcbond_other1.3721.542634
X-RAY DIFFRACTIONr_mcangle_it2.2053.422791
X-RAY DIFFRACTIONr_mcangle_other2.2163.427792
X-RAY DIFFRACTIONr_scbond_it3.2652.207686
X-RAY DIFFRACTIONr_scbond_other3.2642.202685
X-RAY DIFFRACTIONr_scangle_it4.9854.6791002
X-RAY DIFFRACTIONr_scangle_other4.9834.6831003
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.36→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 7 -
Rwork0.276 63 -
obs--3.26 %
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)
11.01780.0916-0.05156.00842.58392.79990.0135-0.1370.02480.1140.04570.02950.0477-0.0147-0.05920.0031-0.0046-0.00150.03930.01040.0106-5.832-5.61237.3297
26.28981.2675-1.03561.6112-0.07582.8037-0.01890.06860.3696-0.02330.0364-0.1003-0.04060.0131-0.01760.001-0.00090.00040.00130.00160.0456-6.6208-5.2149-12.3023
35.45081.60040.77242.0818-0.44622.1758-0.0675-0.036-0.0466-0.05020.0016-0.12530.01320.13460.06590.00720.00520.00390.01520.00240.0087-8.500617.5912-9.7508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 53
2X-RAY DIFFRACTION2B2 - 53
3X-RAY DIFFRACTION3C2 - 53

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