9zdi

Crystal structure of Zn-substituted Rubredoxin from hyperthermophilic bacterium Thermotoga maritima MSB8

Method: X-RAY DIFFRACTION D_max: 47.7 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Rubredoxin

Thermotoga maritima MSB8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–53 Chain B； UniProt 1–53	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；VAPOR DIFFUSION AGAINST 4.0M Ammonium Sulfate, pH 8.5,	Resolution 1.02 Å R-free 0.181

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q9WZC7_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 1–53 Author chain B； PDBConstruct 1–53； UniProt 1–53

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9zdi
Deposition date deposition_date	2025-11-25
Structure title title	Crystal structure of Zn-substituted Rubredoxin from hyperthermophilic bacterium Thermotoga maritima MSB8
Keywords keywords	rubredoxin, electron transfer, hyperthermophilic, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.58 Å
Radius of gyration Rg (electron density) rg_electron	13.34 Å
Forward intensity I(0) i0	3036630.00
Molecular weight molecular_weight	11794.0 kDa
Excluded volume excluded_volume	14465 Å³
Envelope volume envelope_volume	15999 Å³
Hydration-shell volume shell_volume	10523 Å³
Envelope diameter envelope_diameter	46.0 Å
Shell Rg shell_rg	18.67 Å
Envelope Rg envelope_rg	13.61 Å
Shape Rg shape_rg	13.27 Å
Total Rg total_rg	14.62 Å
Total atoms total_atoms	818
Residues n_residues	104
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	47.7 Å
Rg (real space) rg_real	14.53 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	3.0370e+06
I(0) uncertainty (real space) i0_real_error	3.3550e+04
Rg (reciprocal space) rg_reciprocal	14.53 Å
I(0) (reciprocal space) i0_reciprocal	3037000.0000
Solution quality estimate total_estimate	0.8885
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.5 Å
Skewness Skewness skewness	0.248
Kurtosis Kurtosis kurtosis	-0.304
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	376300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Rubredoxin
Molecular weight formula_weight	5989.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	968

MKKYRCKLCGYIYDPEQGDPDSGIEPGTPFEDLPDDWVCPLCGASKEDFEPVE

来源 Source

来源生物 organism	Thermotoga maritima MSB8
NCBI Class编号 ncbi_taxonomy_id	243274
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	108

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8. Citations (1)

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Unit-cell length a length_a	27.018 Å
Unit-cell length b length_b	50.030 Å
Unit-cell length c length_c	33.930 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.020 Å
Low-resolution limit resolution_low	25.270 Å
R factor r_factor	0.1532
R_work r_work	0.1519
R_free r_free	0.1813

fit	/app/data/saxs_computation/zd/9zdi/9zdi.fit
pddf	/app/data/pr_computation/zd/9zdi/9zdi.pr.out
profile	/app/data/saxs_computation/zd/9zdi/9zdi.dat