SAXSdb — 13ld

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

Alanine racemase

Geobacillus stearothermophilus 10

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 1–388 Chain B； UniProt 1–388	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACETATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å R-free 0.204
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–388 Chain D； UniProt 1–388	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACETATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å R-free 0.204

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 13LD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BD0 ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE Deposited 1998-05-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–388（388 aa） Chain B 1–388（388 aa）	Not recorded	IN5 {1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 100MM TRIS BUFFER, PH 8.5, 200MM SODIUM ACETATE, 21% PEG 4000, AND 4MM 1-AMINOETHYL PHOSPHONIC ACID.	Resolution 1.60 Å R-free 0.266
1EPV ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM D-CYCLOSERINE Deposited 2000-03-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–388（387 aa） Chain B 2–388（387 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	DCS D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 4000, sodium acetate, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.226
1FTX Crystal structure of alanine racemase in complex with D-alanine phosphonate Deposited 2000-09-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–388（387 aa） Chain B 2–388（387 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EPC (1S)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]ETHYLPHOSPHONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；23% PEG 4000, 200mM sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.211
1L6F Alanine racemase bound with N-(5'-phosphopyridoxyl)-L-alanine Deposited 2002-03-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–388（388 aa） Chain B 1–388（388 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PP3 ALANYL-PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, sodium acetate, Tris-buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.225
1L6G Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine Deposited 2002-03-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–388（388 aa） Chain B 1–388（388 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PDD N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, sodium acetate, Tris-buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.216
1NIU ALANINE RACEMASE WITH BOUND INHIBITOR DERIVED FROM L-CYCLOSERINE Deposited 2002-12-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–388（388 aa） Chain B 1–388（388 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	DCS D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；23% PEG 4K, 200mM sodium acetate, 100mM tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.20 Å R-free 0.231
1SFT ALANINE RACEMASE Deposited 1996-09-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–388（388 aa） Chain B 1–388（388 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.90 Å R-free 0.267
1XQK Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase Deposited 2004-10-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–382（382 aa） Chain B 1–382（382 aa）	Mutation：Y265F Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Y265F Non-standard monomer：Yes (specific site not provided by mmCIF)	PMH (5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-4-YL)AMINO]METHYL}-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 4K, NaAc, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 398K	Resolution 1.95 Å R-free 0.240
1XQL Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase Deposited 2004-10-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–382（382 aa） Chain B 1–382（382 aa）	Mutation：Y265F Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Y265F Non-standard monomer：Yes (specific site not provided by mmCIF)	PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 2 PMH (5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-4-YL)AMINO]METHYL}-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE × 2 PLP PYRIDOXAL-5'-PHOSPHATE × 2 4AX (R)-4-AMINO-ISOXAZOLIDIN-3-ONE × 2 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 4K, NaAc, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 398K	Resolution 1.80 Å R-free 0.214
2SFP ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR Deposited 1999-02-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–388（388 aa） Chain B 1–388（388 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PLP PYRIDOXAL-5'-PHOSPHATE × 2 PPI PROPANOIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.50	Resolution 1.90 Å R-free 0.259

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ALR_GEOSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–388； UniProt 1–388 Author chain B； PDBConstruct 1–388； UniProt 1–388 Author chain C； PDBConstruct 1–388； UniProt 1–388 Author chain D； PDBConstruct 1–388； UniProt 1–388

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	13ld
Deposition date deposition_date	2026-05-12
最后修订 last_revision	2026-06-10
Structure title title	Deuterated alanine racemase from Geobacillus stearothermophilus
Keywords keywords	deuterated, alanine racemase, isomerase, racemase; ISOMERASE
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	39.22 Å
Radius of gyration Rg (electron density) rg_electron	38.75 Å
Forward intensity I(0) i0	438097000.00
Molecular weight molecular_weight	172760.0 kDa
Excluded volume excluded_volume	217090 Å³
Envelope volume envelope_volume	275030 Å³
Hydration-shell volume shell_volume	59303 Å³
Envelope diameter envelope_diameter	131.3 Å
Shell Rg shell_rg	44.48 Å
Envelope Rg envelope_rg	38.59 Å
Shape Rg shape_rg	38.76 Å
Total Rg total_rg	39.05 Å
Total atoms total_atoms	12189
Residues n_residues	1517
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	126.5 Å
Rg (real space) rg_real	39.13 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	4.3810e+08
I(0) uncertainty (real space) i0_real_error	6.2090e+06
Rg (reciprocal space) rg_reciprocal	39.19 Å
I(0) (reciprocal space) i0_reciprocal	438100000.0000
Solution quality estimate total_estimate	0.9010
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.5 Å
Skewness Skewness skewness	0.225
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	76360000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.913

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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	Alanine racemase
Molecular weight formula_weight	43823.0 kDa
EC 编号 ec_number	5.1.1.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12757

MNDFHRDTWAEVDLDAIYDNVENLRRLLPDDTHIMAVVKANAYGHGDVQVARTALEAGASRLAVAFLDEALALREKGIEAPILVLGASRPADAALAAQQRIALTVFRSDWLEEASALYSGPFPIHFHLKMDTGMGRLGVKDEEETKRIVALIERHPHFVLEGVYTHFATADEVNTDYFSYQYTRFLHMLEWLPSRPPLVHCANSAASLRFPDRTFNMVRFGIAMYGLAPSPGIKPLLPYPLKEAFSLHSRLVHVKKLQPGEKVSYGATYTAQTEEWIGTIPIGYADGWLRRLQHFHVLVDGQKAPIVGRICMDQCMIRLPGPLPVGTKVTLIGRQGDEVISIDDVARHLETINYEVPCTISYRVPRIFFRHKRIMEVRNAIGAGESSA

来源 Source

来源生物 organism	Geobacillus stearothermophilus 10
NCBI Class编号 ncbi_taxonomy_id	272567
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	483

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8. Citations (1)

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Unit-cell length a length_a	85.444 Å
Unit-cell length b length_b	109.925 Å
Unit-cell length c length_c	90.183 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	27.810 Å
R factor r_factor	0.1665
R_work r_work	0.1644
R_free r_free	0.2037

fit	/app/data/saxs_computation/3l/13ld/13ld.fit
pddf	/app/data/pr_computation/3l/13ld/13ld.pr.out
profile	/app/data/saxs_computation/3l/13ld/13ld.dat

Deuterated alanine racemase from Geobacillus stearothermophilus

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

Alanine racemase

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