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1xx8

NMR Structure of the W24A Mutant of the Hyperthermophile Sac7d Protein

Method: SOLUTION NMR Dmax: 39.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sac7d

Sulfolobus acidocaldarius

UniProt P13123

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 0–65 Mutation：W24A No other associated polymer SOLUTION NMR NMR measurement conditions：pH 4.5；303 K；Pressure ambient NMR sample composition：5 mM Sac7d, 90% H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

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.

Other PDB Difference from Current Entry 1XX8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AZP HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX Deposited 1997-11-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–65（65 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.60 Å R-free 0.252
1AZQ HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX Deposited 1997-11-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–65（65 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 1.94 Å R-free 0.238
1BF4 CHROMOSOMAL DNA-BINDING PROTEIN SSO7D/D(GCGAACGC) COMPLEX Deposited 1998-05-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–63（63 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 1.60 Å R-free 0.288
1CA5 INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA Deposited 1999-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–65（65 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.276
1CA6 INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA Deposited 1999-02-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–65（65 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；pH 6.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å R-free 0.257
1SAP HYPERTHERMOPHILE PROTEIN, RELAXATION MATRIX REFINEMENT STRUCTURE Deposited 1995-04-25 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–65（65 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1WD0 Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers Deposited 2004-05-10 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Tris-HCl, PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.257
1WD1 Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers Deposited 2004-05-10 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；potassium phosphate, PEG8000, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.290
1WTO Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29F in complex with DNA GCGATCGC Deposited 2004-11-29 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Mutation：V26F/M29F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 400, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 1.50 Å R-free 0.231
1WTP Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA GCGA(UBr)CGC Deposited 2004-11-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 0–65（66 aa）
Chain B 0–65（66 aa）
Mutation：M29F Mutation：M29F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 400, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 1.90 Å R-free 0.287
1WTQ Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA GTAATTAC Deposited 2004-11-29 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Mutation：M29F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 400, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 1.70 Å R-free 0.225
1WTR Hyperthermophile chromosomal protein SAC7D single mutant M29A in complex with DNA GCGATCGC Deposited 2004-11-29 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Mutation：M29A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 400, Tris buffer , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 1.80 Å R-free 0.274
1WTV Hyperthermophile chromosomal protein SAC7D single mutant M29A in complex with DNA GTAATTAC Deposited 2004-11-29 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Mutation：M29A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 400, Tris buffer , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 1.60 Å R-free 0.238
1WTW Hyperthermophile chromosomal protein SAC7D single mutant V26A in complex with DNA GCGATCGC Deposited 2004-11-29 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Mutation：V26A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 400, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 2.20 Å R-free 0.286
1WTX Hyperthermophile chromosomal protein SAC7D single mutant V26A in complex with DNA GTAATTAC Deposited 2004-11-29 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Mutation：V26A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 400, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Resolution 2.20 Å R-free 0.253
1WVL Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA decamer Deposited 2004-12-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric
Chain not uniquely mapped Reference range not declared
Chain A 0–65（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.6M Tri-Sodium Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.269
1XYI Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex with DNA GCGATCGC Deposited 2004-11-10 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 0–65（66 aa）
Mutation：V26A, M29A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298 K；Tris, PEG400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.45 Å R-free 0.255
2XIW Crystal structure of the Sac7d-derived IgG1-binder C3-C24S Deposited 2010-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–66（65 aa）
Chain B 2–66（65 aa）
Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 3.5 M (NH4)2SO4
Resolution 1.50 Å R-free 0.191
8CMN 18mer DNA mimic Foldamer with an aliphatic linker in complex with Sac7d wild protein Deposited 2023-02-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: monomeric
Chain AA 1–66（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；10% PEG 400, 0.1 M MES pH 6.0
Resolution 2.65 Å R-free 0.297
8Q2M 18mer DNA mimic Foldamer with an Aliphatic linker in complex with Sac7d V26A/M29A protein Deposited 2023-08-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain AA 1–66（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；9 % PEG 400, 0.1 M MES pH 6.0
Resolution 3.21 Å R-free 0.335
8QPC 18mer DNA mimic Foldamer with an Aromatic linker in complex with Sac7d V26A/M29A protein Deposited 2023-10-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: monomeric
Chain AA 1–66（66 aa）
Mutation：V26A/M29A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293.15 K；10 % PEG 400, 0.1 M MES pH 6.0
Resolution 3.24 Å R-free 0.348
9HIZ Complex of the Nanofitin Sac7d-C3(C24A) with a human IgG1 Fc fragment Deposited 2024-11-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 2–66（65 aa）
Chain S 2–66（65 aa）
Chain T 2–66（65 aa）
Chain U 2–66（65 aa）
Mutation：K7L,Y8L,K9N,K21R,K22D,W24A,V26Q,M29N,S31K,T33L,D35N,T40Y,R42A,A44N,S46D Mutation：K7L,Y8L,K9N,K21R,K22D,W24A,V26Q,M29N,S31K,T33L,D35N,T40Y,R42A,A44N,S46D Mutation：K7L,Y8L,K9N,K21R,K22D,W24A,V26Q,M29N,S31K,T33L,D35N,T40Y,R42A,A44N,S46D Mutation：K7L,Y8L,K9N,K21R,K22D,W24A,V26Q,M29N,S31K,T33L,D35N,T40Y,R42A,A44N,S46D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；24 % (w/v) PEG8000, 0.1 M Tris/HCl pH 8.5
Resolution 2.90 Å R-free 0.279
9QT7 Crystal structure of affitin C10 fused to a coiled-coil domain in complex with a quinoline oligoamide foldamer Deposited 2025-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–65（64 aa）
Chain B 2–65（64 aa）
Chain C 2–65（64 aa）
Chain D 2–65（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；20% PEG 400 0.1M Sodium cacodylate pH 6.5
Resolution 2.80 Å R-free 0.296
9QT7 Crystal structure of affitin C10 fused to a coiled-coil domain in complex with a quinoline oligoamide foldamer Deposited 2025-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–65（64 aa）
Chain D 2–65（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；20% PEG 400 0.1M Sodium cacodylate pH 6.5
Resolution 2.80 Å R-free 0.296
9QT7 Crystal structure of affitin C10 fused to a coiled-coil domain in complex with a quinoline oligoamide foldamer Deposited 2025-04-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 2–65（64 aa）
Chain C 2–65（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；20% PEG 400 0.1M Sodium cacodylate pH 6.5
Resolution 2.80 Å R-free 0.296

23 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DN71_SULAC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–66； UniProt 0–65

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

SAXS profile for 1xx8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1xx8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1xx8
Deposition date deposition_date2004-11-04
Structure title titleNMR Structure of the W24A Mutant of the Hyperthermophile Sac7d Protein
Keywords keywordshyperthermophile, DNA-binding protein, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.11 Å
Radius of gyration Rg (electron density) rg_electron11.75 Å
Forward intensity I(0) i096272000.00
Molecular weight molecular_weight82498.0 kDa
Excluded volume excluded_volume104080 ų
Envelope volume envelope_volume17789 ų
Hydration-shell volume shell_volume11428 ų
Envelope diameter envelope_diameter43.6 Å
Shell Rg shell_rg19.01 Å
Envelope Rg envelope_rg13.63 Å
Shape Rg shape_rg11.69 Å
Total Rg total_rg12.26 Å
Total atoms total_atoms11891
Residues n_residues726
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax39.5 Å
Rg (real space) rg_real12.07 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real9.6270e+07
I(0) uncertainty (real space) i0_real_error9.5080e+05
Rg (reciprocal space) rg_reciprocal12.07 Å
I(0) (reciprocal space) i0_reciprocal96270000.0000
Solution quality estimate total_estimate0.7939
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.0 Å
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.182
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha104000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1xx8a_
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.13 — Chromo domain-like
Family Family familyb.34.13.1 — Histone-like proteins from archaea

CATH v4.4 (1 domains)

Domain ID domain_id1xx8A00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)