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- PDB-9zdp: Crystal structure of rubredoxin from psychrophilic bacterium Pola... -

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Basic information

Entry
Database: PDB / ID: 9zdp
TitleCrystal structure of rubredoxin from psychrophilic bacterium Polaromonas glacialis
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / electron transfer / psychrophilic
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 speciesPolaromonas glacialis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsDoukov, T.I. / George, D. / Cole, C. / Drumright, K. / 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 26, 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
D: Rubredoxin
E: Rubredoxin
F: Rubredoxin
G: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,49715
Polymers42,0837
Non-polymers4148
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: 7 major anomalous peaks
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.897, 73.897, 199.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11D-246-

HOH

21G-213-

HOH

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Components

#1: Protein
Rubredoxin


Mass: 6011.924 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas glacialis (bacteria) / Gene: ABLV49_04330
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0AAU7LTP7
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.25 Å3/Da / Density % sol: 62.21 % / Description: Thin plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION AGAINST 1.5 M AMMONIUM SULFATE, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostat / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.83→69.29 Å / Num. obs: 36053 / % possible obs: 95.3 % / Redundancy: 54.1 % / Biso Wilson estimate: 20.709 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.054 / Net I/σ(I): 14.1
Reflection shellResolution: 1.83→2.042 Å / Redundancy: 47.9 % / Rmerge(I) obs: 6.053 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1803 / CC1/2: 0.608 / Rpim(I) all: 0.862 / % possible all: 69.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.83→69.29 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.876 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1837 5.1 %RANDOM
Rwork0.17069 ---
obs0.17226 34216 72.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.029 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.83→69.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 0 223 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123017
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162625
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.7754113
X-RAY DIFFRACTIONr_angle_other_deg0.5571.7356107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.49657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74410471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it4.0155.9241479
X-RAY DIFFRACTIONr_mcbond_other4.0135.9221479
X-RAY DIFFRACTIONr_mcangle_it4.94113.2481837
X-RAY DIFFRACTIONr_mcangle_other4.95813.2491838
X-RAY DIFFRACTIONr_scbond_it7.4876.9561538
X-RAY DIFFRACTIONr_scbond_other7.4856.9581539
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.86115.2892276
X-RAY DIFFRACTIONr_long_range_B_refined9.48242.213577
X-RAY DIFFRACTIONr_long_range_B_other9.4841.23534
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.834→1.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 3 -
Rwork0.298 58 -
obs--1.7 %
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)
11.9604-1.1336-1.66846.97520.39115.90350.11680.223-0.0272-0.362-0.13990.104-0.12280.01490.02310.04370.00980.01060.0584-0.01570.0193-43.19763.23724.728
24.07240.971-0.06456.85670.69576.81610.1641-0.31490.44920.476-0.08490.1264-0.66320.0062-0.07920.16010.00720.05710.0329-0.02250.0682-32.04971.817-2.866
37.82950.2127-1.00063.71321.00013.7240.01250.2095-0.2671-0.134-0.04330.33820.1216-0.38020.03080.03690.0040.0090.06680.00740.0844-45.19158.159-15.891
43.27680.89280.75864.2017-0.133811.98360.011-0.053-0.07620.01260.02510.0705-0.1297-0.0351-0.03610.0312-0.00480.02360.0122-0.00410.0231-31.1553.5788.125
54.71091.70710.23089.37662.786.0521-0.20190.09830.3677-0.26930.04310.4289-0.1502-0.41390.15880.03060.0138-0.03480.0445-0.00450.0475-12.44165.20514.801
69.85581.5755-2.01915.94770.51672.59010.06980.0226-0.38640.1555-0.09880.04540.1412-0.15980.0290.04020.0075-0.00810.0249-0.0010.0198-32.71739.34922.931
75.0998-0.6621-0.930810.2226-1.52888.87130.2040.33750.9286-0.8565-0.2054-0.5514-0.82920.16990.00140.25780.04410.01520.07520.00560.2853-2.76382.6556.965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 53
2X-RAY DIFFRACTION1A101
3X-RAY DIFFRACTION2B1 - 53
4X-RAY DIFFRACTION2B101 - 102
5X-RAY DIFFRACTION3C1 - 53
6X-RAY DIFFRACTION3C101
7X-RAY DIFFRACTION4D1 - 53
8X-RAY DIFFRACTION4D101
9X-RAY DIFFRACTION5E1 - 53
10X-RAY DIFFRACTION5E101
11X-RAY DIFFRACTION6F1 - 53
12X-RAY DIFFRACTION6F101
13X-RAY DIFFRACTION7G1 - 53
14X-RAY DIFFRACTION7G101

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