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9xwu

Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with AMP

Method: X-RAY DIFFRACTION Dmax: 112.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CDP-diacylglycerol pyrophosphatase

Escherichia coli K-12

UniProt P06282

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 1–251 Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1M HEPES (pH 7.5), 0.2M sodium chloride, 25% polyethylene glycol 3350 Resolution 2.00 Å R-free 0.253
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–251 Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1M HEPES (pH 7.5), 0.2M sodium chloride, 25% polyethylene glycol 3350 Resolution 2.00 Å R-free 0.253

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 9XWU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9XWV Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with CMP Deposited 2025-11-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–251（251 aa）
Not recorded C5P CYTIDINE-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1M Tris (pH 8.5), 0.2M magnesium chloride hexahydrate, 25% polyethylene glycol 3350, 30% trimethylamine N-oxide dihydrate
Resolution 1.94 Å R-free 0.235
9XWV Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with CMP Deposited 2025-11-28 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–251（251 aa）
Not recorded C5P CYTIDINE-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1M Tris (pH 8.5), 0.2M magnesium chloride hexahydrate, 25% polyethylene glycol 3350, 30% trimethylamine N-oxide dihydrate
Resolution 1.94 Å R-free 0.235

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDH_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–251； UniProt 1–251 Author chain B； PDBConstruct 1–251； UniProt 1–251

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 9xwu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xwu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9xwu
Deposition date deposition_date2025-11-28
Structure title titleCrystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with AMP
Keywords keywords;CDP-diacylglycerol, Phosphatidic acid, Bitopic membrane protein, CDP-DAG hydrolase, bacterial phospholipid metabolism, AMP bound structure, inhibitor bound, HYDROLASE ;; HYDROLASE
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_guinier40.68 Å
Radius of gyration Rg (electron density) rg_electron40.35 Å
Forward intensity I(0) i043152900.00
Molecular weight molecular_weight51496.0 kDa
Excluded volume excluded_volume63652 ų
Envelope volume envelope_volume93551 ų
Hydration-shell volume shell_volume19116 ų
Envelope diameter envelope_diameter121.1 Å
Shell Rg shell_rg47.63 Å
Envelope Rg envelope_rg38.06 Å
Shape Rg shape_rg40.34 Å
Total Rg total_rg40.78 Å
Total atoms total_atoms3616
Residues n_residues446
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 dmax112.8 Å
Rg (real space) rg_real41.02 Å
Rg uncertainty (real space) rg_real_error1.28 Å
I(0) (real space) i0_real4.3150e+07
I(0) uncertainty (real space) i0_real_error8.0240e+05
Rg (reciprocal space) rg_reciprocal40.68 Å
I(0) (reciprocal space) i0_reciprocal43140000.0000
Solution quality estimate total_estimate0.5445
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.1 Å
Skewness Skewness skewness0.148
Kurtosis Kurtosis kurtosis-1.484
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4346000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.012; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.040; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)