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4qnm

CRYSTAL STRUCTURE of PSPF(1-265) E108Q MUTANT

Method: X-RAY DIFFRACTION Dmax: 78.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Psp operon transcriptional activator

Escherichia coli

UniProt P37344

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 1–265 Fragment：Phage Shock protein F AAA DOMAIN, RESIDUES 1-265 Mutation：E108Q EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；100mM Bis-Tris pH 8.0, 12-16% MPD, 2M Ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 1.63 Å R-free 0.203

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 4QNM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2BJV Crystal Structure of PspF(1-275) R168A mutant Deposited 2005-02-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–265（265 aa） Fragment：AAA DOMAIN, RESIDUES 1-265
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2 M AMMONIUM FORMATE, 0.1 MM HEPES PH 8.0, 10% MPD
Resolution 1.70 Å R-free 0.212
2BJW PspF AAA domain Deposited 2005-02-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–265（265 aa） Fragment：AAA DOMAIN, RESIDUES 1-265
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2.0 M AMMONIUM FORMATE, 0.1 M HEPES PH 8.0, 10% MPD
Resolution 1.75 Å R-free 0.208
2C96 Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF Deposited 2005-12-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–265（265 aa） Fragment：AAA DOMAIN, RESIDUES 1-265
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2M AMMONIUM FORMATE, 0.1 M HEPES PH 8.0, 5% MPD
Resolution 1.80 Å R-free 0.246
2C98 Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF Deposited 2005-12-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–265（265 aa） Fragment：AAA DOMAIN, RESIDUES 1-265
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2M AMMONIUM FORMATE, 0.1 M HEPES PH 8.0, 5% MPD
Resolution 1.90 Å R-free 0.203
2C99 Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF Deposited 2005-12-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–265（265 aa） Fragment：AAA DOMAIN, RESIDUES 1-265
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2M AMMONIUM FORMATE, 0.1 M HEPES PH 8.0, 5% MPD
Resolution 1.90 Å R-free 0.212
2C9C Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF Deposited 2005-12-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–265（265 aa） Fragment：AAA DOMAIN, RESIDUES 1-265
Mutation：YES MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；2M AMMONIUM FORMATE, 0.1 M HEPES PH 8.0, 5% MPD
Resolution 2.10 Å R-free 0.198
2VII PspF1-275-Mg-AMP Deposited 2007-12-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–259（259 aa） Fragment：AAA DOMAIN, RESIDUES 1-259
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.1M TRIS-HCL PH 8.0, 2.0M AMMONIUM FORMATE, 10% MPD
Resolution 2.85 Å R-free 0.241
4QNR CRYSTAL STRUCTURE OF PSPF(1-265) E108Q MUTANT bound to ATP Deposited 2014-06-18 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–265（265 aa） Fragment：Phage Shock protein F AAA DOMAIN, RESIDUES 1-265
Mutation：E108Q ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；100mM Bis-Tris pH 8.0, 12-16% MPD, 2M Ammonium formate , VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.54 Å R-free 0.178
4QOS CRYSTAL STRUCTURE OF PSPF(1-265) E108Q MUTANT bound to ADP Deposited 2014-06-20 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–265（265 aa） Fragment：Phage Shock protein F AAA DOMAIN, RESIDUES 1-265
Mutation：E108Q ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；100mM Bis-Tris pH 8.0, 12-16% MPD, 2M Ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.42 Å R-free 0.190
5NSS Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex Deposited 2017-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: octameric
Chain F 1–275（275 aa）
Chain G 1–275（275 aa）
Chain J 1–275（275 aa）
Chain K 1–275（275 aa）
Chain L 1–275（275 aa）
Chain N 1–275（275 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.80 Å
9Q90 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain 1 1–275（275 aa）
Chain 2 1–275（275 aa）
Chain 3 1–275（275 aa）
Chain 4 1–275（275 aa）
Chain 5 1–275（275 aa）
Chain 6 1–275（275 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 4 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9Q91 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 6 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain 1 1–259（259 aa）
Chain 2 1–259（259 aa）
Chain 3 1–259（259 aa）
Chain 4 1–259（259 aa）
Chain 5 1–259（259 aa）
Chain 6 1–259（259 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
9Q92 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 5 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain 1 1–259（259 aa）
Chain 2 1–259（259 aa）
Chain 3 1–259（259 aa）
Chain 4 1–259（259 aa）
Chain 5 1–259（259 aa）
Chain 6 1–259（259 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
9Q93 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain 1 1–259（259 aa）
Chain 2 1–259（259 aa）
Chain 3 1–259（259 aa）
Chain 4 1–259（259 aa）
Chain 5 1–259（259 aa）
Chain 6 1–259（259 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
9Q94 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 3 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain 1 1–275（275 aa）
Chain 2 1–275（275 aa）
Chain 3 1–275（275 aa）
Chain 4 1–275（275 aa）
Chain 5 1–275（275 aa）
Chain 6 1–275（275 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.80 Å
9Q95 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain 1 1–275（275 aa）
Chain 2 1–275（275 aa）
Chain 3 1–275（275 aa）
Chain 4 1–275（275 aa）
Chain 5 1–275（275 aa）
Chain 6 1–275（275 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.80 Å
9Q97 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 2 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain 1 1–259（259 aa）
Chain 2 1–259（259 aa）
Chain 3 1–259（259 aa）
Chain 4 1–259（259 aa）
Chain 5 1–259（259 aa）
Chain 6 1–259（259 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9Q98 CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1 Deposited 2025-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain 1 1–259（259 aa）
Chain 2 1–259（259 aa）
Chain 3 1–259（259 aa）
Chain 4 1–259（259 aa）
Chain 5 1–259（259 aa）
Chain 6 1–259（259 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 AF3 ALUMINUM FLUORIDE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.30 Å

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PSPF_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–265； UniProt 1–265

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 4qnm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4qnm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4qnm
Deposition date deposition_date2014-06-18
Structure title titleCRYSTAL STRUCTURE of PSPF(1-265) E108Q MUTANT
Keywords keywords;AAA domain, Transcriptional activator for the phage shock protein (psp) operon (pspABCDE) and pspG gene, ATP Binding, DNA binding, TRANSCRIPTION ;; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.31 Å
Radius of gyration Rg (electron density) rg_electron21.40 Å
Forward intensity I(0) i012695700.00
Molecular weight molecular_weight26975.0 kDa
Excluded volume excluded_volume33895 ų
Envelope volume envelope_volume41492 ų
Hydration-shell volume shell_volume17152 ų
Envelope diameter envelope_diameter78.5 Å
Shell Rg shell_rg26.72 Å
Envelope Rg envelope_rg21.65 Å
Shape Rg shape_rg21.43 Å
Total Rg total_rg22.06 Å
Total atoms total_atoms1923
Residues n_residues238
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 dmax78.4 Å
Rg (real space) rg_real22.41 Å
Rg uncertainty (real space) rg_real_error0.91 Å
I(0) (real space) i0_real1.2700e+07
I(0) uncertainty (real space) i0_real_error1.8090e+05
Rg (reciprocal space) rg_reciprocal22.39 Å
I(0) (reciprocal space) i0_reciprocal12700000.0000
Solution quality estimate total_estimate0.8534
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.4 Å
Skewness Skewness skewness0.446
Kurtosis Kurtosis kurtosis-0.355
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2140000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.755; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.832; Smooth: 0.994
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4qnmA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id4qnmA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily60 —
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8. Citations (1)

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9. Files and Curves (10)