5ls7

Complex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: GOOD

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

Aspartate 1-decarboxylase

Escherichia coli K-12

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 heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–24 Chain D； UniProt 25–126	Non-standard monomer：Yes (specific site not provided by mmCIF)	PanD maturation factor × 4 （P37613） GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 8 ACO ACETYL COENZYME A × 4 MG MAGNESIUM ION × 4 CO2* CARBON DIOXIDE × 12 SCN THIOCYANATE ION × 8 74C methyl radical × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；200 mM KSCN, 100 mM Bis-Tris propane pH 6.5, 20% v/v PEG 3350	Resolution 1.16 Å R-free 0.137

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 5LS7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AW8 PYRUVOYL DEPENDENT ASPARTATE DECARBOXYLASE Deposited 1997-10-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–24（24 aa） Chain B 25–115（91 aa） Chain D 1–24（24 aa） Chain E 25–115（91 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PROTEIN WAS CRYSTALLIZED FROM 12% PEG 2000 MME, 0.1 M NA ACETATE, PH 4.6	Resolution 2.20 Å R-free 0.239
1PPY Native precursor of pyruvoyl dependent Aspartate decarboxylase Deposited 2003-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa） Chain B 1–126（126 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；NH42SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.95 Å R-free 0.195
1PQE S25A mutant of pyruvoyl dependent aspartate decarboxylase Deposited 2003-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa）	Mutation：S25A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；NH42SO4,Tris/HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.95 Å R-free 0.205
1PQF Glycine 24 to Serine mutation of aspartate decarboxylase Deposited 2003-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa） Chain B 1–126（126 aa）	Mutation：G24S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G24S Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；NH42SO4, citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.185
1PQH Serine 25 to Threonine mutation of aspartate decarboxylase Deposited 2003-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa） Chain B 1–126（126 aa）	Mutation：S25T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S25T Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2 MLA MALONIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；292 K；Sodium malonate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.29 Å R-free 0.166
1PT0 Unprocessed Pyruvoyl Dependent Aspartate Decarboxylase with an Alanine insertion at position 26 Deposited 2003-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa） Chain B 1–126（126 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；290 K；1.4-1.6M Ammonium Sulphate, 0.1M Citric Acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.191
1PT1 Unprocessed Pyruvoyl Dependent Aspartate Decarboxylase with Histidine 11 Mutated to Alanine Deposited 2003-06-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa） Chain B 1–126（126 aa）	Mutation：H11A Mutation：H11A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；290 K；1.4-1.6M Ammonium Sulphate, 0.1M Citric Acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.90 Å R-free 0.170
1PYQ Unprocessed Aspartate Decarboxylase Mutant, with Alanine inserted at position 24 Deposited 2003-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa） Chain B 1–126（126 aa）	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；290 K；0.1M citric acid, 1.6M ammonium sulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.90 Å R-free 0.179
1PYU Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys Deposited 2003-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–24（24 aa） Chain B 25–126（102 aa） Chain C 1–24（24 aa） Chain D 25–126（102 aa）	Mutation：S25C Mutation：S25C	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；290 K；0.1M citric acid, 1.6M ammonium sulphate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.90 Å R-free 0.196
3TM7 Processed Aspartate Decarboxylase Mutant with Asn72 mutated to Ala Deposited 2011-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–24（24 aa） Chain B 25–126（102 aa） Chain C 1–24（24 aa） Chain D 25–126（102 aa）	Mutation：N72A Mutation：N72A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；1.6-2.4M ammonium sulphate, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.184
3TM7 Processed Aspartate Decarboxylase Mutant with Asn72 mutated to Ala Deposited 2011-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–24（24 aa） Chain B 25–126（102 aa） Chain C 1–24（24 aa） Chain D 25–126（102 aa）	Mutation：N72A Mutation：N72A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；1.6-2.4M ammonium sulphate, 0.1M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.184
4AOK Conformational dynamics of aspartate alpha-decarboxylase active site revealed by protein-ligand complexes: 1-methyl-L-aspartate complex Deposited 2012-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–24（24 aa） Chain B 25–126（102 aa） Chain D 1–24（24 aa） Chain E 25–126（102 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.2；5 MG/ML ASPARTATE-ALPHA-DECARBOXYLASE IN 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH 3.8	Resolution 1.50 Å R-free 0.180
4AON Conformational dynamics of aspartate alpha-decarboxylase active site revealed by protein-ligand complexes: 1-methyl-L-aspartate complex Deposited 2012-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–24（24 aa） Chain B 25–126（102 aa） Chain D 1–24（24 aa） Chain E 25–126（102 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GLU GLUTAMIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.2；5 MG/ML ASPARTATE-ALPHA-DECARBOXYLASE IN 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH 3.8	Resolution 1.50 Å R-free 0.162
4AZD T57V mutant of aspartate decarboxylase Deposited 2012-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–126（126 aa） Chain B 1–126（126 aa）	Mutation：YES Mutation：YES	MLI MALONATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；292 K；2.4 M SODIUM MALONATE, 1.5 M (NH4)2SO4 PH 4, 292 K	Resolution 1.62 Å R-free 0.217
4CRY Direct visualisation of strain-induced protein post-translational modification Deposited 2014-03-02	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–24（24 aa） Chain G 25–126（102 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE	Resolution 1.61 Å R-free 0.150
4CRZ Direct visualisation of strain-induced protein prost-translational modification Deposited 2014-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–126（126 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 4 ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE	Resolution 1.70 Å R-free 0.175
4CS0 Direct visualisation of strain-induced protein post-translational modification Deposited 2014-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–126（126 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 4 ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE	Resolution 2.10 Å R-free 0.237
4D7Z E. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resolution of 1.9 Angstroms Deposited 2014-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–24（24 aa） Chain B 25–119（95 aa） Fragment：RESIDUES 25-119	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	PEG DI(HYDROXYETHYL)ETHER × 1 SCN THIOCYANATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；ADC.PANZ COMPLEX WAS PREPARED IN A 10: 11 RATIO AT A FINAL CONCENTRATION OF 5.7 MG/ML WITH A 2-FOLD MOLAR EXCESS (RELATIVE TO PANZ) OF ACETYLCOA IN 0.05 M TRIS-HCL PH 7.69, 0.1 M NACL, 0.1 MM DTT. THIS WAS MIXED IN A 1:1 RATIO WITH RESERVOIR SOLUTION (0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS- TRIS PROPANE PH 6.8, 20 % W/V PEG 3350) AND CRYSTALLIZED BY HANGING DROP VAOUR DIFFUSION (4 UL DROPLET OVER A 1 ML RESERVOIR).	Resolution 1.90 Å R-free 0.244

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

View Construct and Data Evidence

UniProt name	PAND_ECOLI
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 18–41； UniProt 1–24 Author chain D； PDBConstruct 1–102； UniProt 25–126

PanD maturation factor

Escherichia coli K-12

UniProt P37613

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 heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain B； UniProt 1–127	Not recorded	Aspartate 1-decarboxylase × 4 （P0A790） Aspartate 1-decarboxylase × 4 （P0A790） GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 8 ACO ACETYL COENZYME A × 4 MG MAGNESIUM ION × 4 CO2* CARBON DIOXIDE × 12 SCN THIOCYANATE ION × 8 74C methyl radical × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；200 mM KSCN, 100 mM Bis-Tris propane pH 6.5, 20% v/v PEG 3350	Resolution 1.16 Å R-free 0.137

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5LS7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2K5T Solution NMR Structure of Putative N-Acetyl Transferase YhhK from E. coli Bound to Coenzyme A: Northeast Structural Genomics Consortium Target ET106 Deposited 2008-06-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–127（127 aa）	Mutation：A119T	COA COENZYME A × 1	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 300；Pressure ambient NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] YhhK, 5 mM Coenzyme A, 7 % D2O, 300 mM sodium chloride, 25 mM TRIS, 5 mM DTT, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] YhhK, 5 mM Coenzyme A, 100 % D2O, 300 mM sodium chloride, 25 mM TRIS, 5 mM DTT, 100% D2O \| 100% D2O	Resolution not provided
4CRY Direct visualisation of strain-induced protein post-translational modification Deposited 2014-03-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–127（127 aa）	Not recorded	ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE	Resolution 1.61 Å R-free 0.150
4CRZ Direct visualisation of strain-induced protein prost-translational modification Deposited 2014-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–127（127 aa）	Not recorded	SCN THIOCYANATE ION × 4 ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE	Resolution 1.70 Å R-free 0.175
4CS0 Direct visualisation of strain-induced protein post-translational modification Deposited 2014-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1–127（127 aa）	Not recorded	SCN THIOCYANATE ION × 4 ACO ACETYL COENZYME *A × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；20% (W/V) POLYETHYLENE GLYCOL (PEG) 3350, 0.1 M BIS-TRIS PROPANE PH 7.4, 0.2 M POTASSIUM THIOCYANATE	Resolution 2.10 Å R-free 0.237

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PANM_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–127； UniProt 1–127

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	5ls7
Deposition date deposition_date	2016-08-22
Structure title title	Complex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ
Keywords keywords	protein derived cofactor, coenzyme A biosynthesis, protein complex, metabolic pathway regulation, LYASE; LYASE
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	22.17 Å
Radius of gyration Rg (electron density) rg_electron	21.15 Å
Forward intensity I(0) i0	17200400.00
Molecular weight molecular_weight	29799.0 kDa
Excluded volume excluded_volume	36672 Å³
Envelope volume envelope_volume	44510 Å³
Hydration-shell volume shell_volume	18336 Å³
Envelope diameter envelope_diameter	75.2 Å
Shell Rg shell_rg	26.65 Å
Envelope Rg envelope_rg	21.22 Å
Shape Rg shape_rg	21.17 Å
Total Rg total_rg	21.84 Å
Total atoms total_atoms	2082
Residues n_residues	253
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	73.2 Å
Rg (real space) rg_real	22.18 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.7200e+07
I(0) uncertainty (real space) i0_real_error	2.3790e+05
Rg (reciprocal space) rg_reciprocal	22.18 Å
I(0) (reciprocal space) i0_reciprocal	17200000.0000
Solution quality estimate total_estimate	0.8936
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.301
Kurtosis Kurtosis kurtosis	-0.524
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2276000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Aspartate 1-decarboxylase
Molecular weight formula_weight	4770.6 kDa
EC 编号 ec_number	4.1.1.11
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2506

MRGSHHHHHHGLVPRGSMIRTMLQGKLHRVKVTHADLHYEG

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PanD maturation factor
Molecular weight formula_weight	15738.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKLTIIRLEKFSDQDRIDLQKIWPEYSPSSLQVDDNHRIYAARFNERLLAAVRVTLSGTEGALDSLRVREVTRRRGVGQYLLEEVLRNNPGVSCWWMADAGVEDRGVMTAFMQALGFTAQQGGWEKCSGLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Aspartate 1-decarboxylase
Molecular weight formula_weight	11044.3 kDa
EC 编号 ec_number	4.1.1.11
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

XCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRTAKAIPVQVA

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	ACETYL COENZYME *A
Molecular weight formula_weight	809.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CARBON DIOXIDE
Molecular weight formula_weight	44.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	methyl radical
Molecular weight formula_weight	15.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	292

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ls7B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	5ls7D00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

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8. Citations (1)

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Unit-cell length a length_a	85.863 Å
Unit-cell length b length_b	85.863 Å
Unit-cell length c length_c	80.055 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	1.160 Å
Low-resolution limit resolution_low	29.280 Å
R factor r_factor	0.1146
R_work r_work	0.1134
R_free r_free	0.1369

fit	/app/data/saxs_computation/ls/5ls7/5ls7.fit
pddf	/app/data/pr_computation/ls/5ls7/5ls7.pr.out
profile	/app/data/saxs_computation/ls/5ls7/5ls7.dat

Complex of wild type E. coli alpha aspartate decarboxylase with its processing factor PanZ

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

Aspartate 1-decarboxylase

State in the Current Structure

Other States of the Same Protein in the Database

PanD maturation factor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)