7rst

The Crystal Structure of Recombinant Chloroperoxidase Expressed in Aspergillus niger

Method: X-RAY DIFFRACTION D_max: 61.5 Å Quality: GOOD

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

Chloroperoxidase

Leptoxyphium fumago

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 3 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–319	Non-standard monomer：Yes (specific site not provided by mmCIF)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 1 MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 12 IOD IODIDE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M NaI, 20% polyethyleneglycol (PEG) 3350	Resolution 1.69 Å R-free 0.210

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 7RST	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CPO CHLOROPEROXIDASE Deposited 1996-02-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–319（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 9 XYS alpha-D-xylopyranose × 1 MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.224
2CIV Chloroperoxidase bromide complex Deposited 2006-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAN alpha-D-mannopyranose × 10 BR BROMIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；22 % PEG3000, 0.1 M KBR, 0.1 M CITRATE PH 3.6	Resolution 1.80 Å R-free 0.184
2CIW Chloroperoxidase iodide complex Deposited 2006-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAN alpha-D-mannopyranose × 11 IOD IODIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；20 % PEG 3350, 50 MM NAI, 0.1 M SODIUM CITRATE PH 3.6	Resolution 1.15 Å R-free 0.171
2CIX chloroperoxidase complexed with cyclopentanedione Deposited 2006-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 10 EDO 1,2-ETHANEDIOL × 1 CEJ CYCLOPENTANE-1,3-DIONE × 1 BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；ML: 22 % PEG3000, 0.1 M KBR, 0.1 M CITRATE PH 3.6 CRYSTALS WERE SOAKED IN ML SUPPLEMENTED WITH 200 MM CYCLOPENTANEDIONE, 10 % DMSO	Resolution 1.80 Å R-free 0.217
2CIY Chloroperoxidase complexed with cyanide and DMSO Deposited 2006-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 11 BR BROMIDE ION × 2 EDO 1,2-ETHANEDIOL × 1 CYN CYANIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；CRYSTALLISATION CONDITIONS: 22 % PEG 3000, 0.1 M KBR, 0.1 M CITRATE PH 3.6 CRYSTALS WERE SOAKED IN 50 MM KCN, 200 MM CYCLOPENTANEDIONE, 10 % DMSO, 22 % PEG3000, 0.1 M SODIUM CITRATE PH 6 FOR 10 MIN AT ROOM TMEPERATURE	Resolution 1.70 Å R-free 0.204
2CIZ chloroperoxidase complexed with acetate Deposited 2006-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 9 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 2 BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；CRYSTALS WERE SOAKED IN 300 MM ACETIC ACID, 50 MM KBR, 22 % PEG3000, 0.1 M CITRATE PH 3.6 FOR 10 MIN AT ROOM TEMPERATURE	Resolution 1.30 Å R-free 0.170
2CJ0 chloroperoxidase complexed with nitrate Deposited 2006-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 12 EDO 1,2-ETHANEDIOL × 3 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 50 MM MG(NO3)2, 20 % PEG 3000, 0.1 M SODIUM CITRATE PH3.6	Resolution 1.75 Å R-free 0.207
2CJ1 chloroperoxidase complexed with formate (ethylene glycol cryoprotectant) Deposited 2006-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAN alpha-D-mannopyranose × 12 EDO 1,2-ETHANEDIOL × 3 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；100 MM SODIUM FORMATE, 24 % PEG 3000, 0.1 M CITRATE PH 3.6 CRYOPROTECTANT CONTAINED 15 % ETHYLENE GLYCOL	Resolution 1.70 Å R-free 0.229
2CJ2 chloroperoxidase complexed with formate (sugar cryoprotectant) Deposited 2006-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 10 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；100 MM SODIUM FORMATE, 24 % PEG 3000, 0.1 M SODIUM CITRATE PH 3.6 CRYOPROTECTANT: ML SUPPLEMENTED WITH 10 % XYLITOL, 10 % SUCROSE	Resolution 1.60 Å R-free 0.204
2CPO CHLOROPEROXIDASE Deposited 1996-02-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–319（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 8 MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.228
2J18 Chloroperoxidase mixture of ferric and ferrous states (low dose data set) Deposited 2006-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–319（298 aa） Fragment：RESIDUES 22-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 9 BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.4；50MM KBR, 20% PEG3000, 0.1 M SODIUM CITRATE PH3.4, pH 3.40	Resolution 1.75 Å R-free 0.206
2J19 Ferrous Chloroperoxidase (high dose data set) Deposited 2006-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–319（298 aa） Fragment：RESIDUES 22-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 9 BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.4；50MM KBR, 20% PEG3000, 0.1 SODIUM CITRATE PH 3.4	Resolution 1.75 Å R-free 0.204
2J5M Structure of Chloroperoxidase Compound 0 Deposited 2006-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 PEO HYDROGEN PEROXIDE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 10 EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；22 % PEG3000, 0.1 M KBR, 0.1 M NA CITRATE PH 3.6	Resolution 1.75 Å R-free 0.210

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRXC_LEPFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–299； UniProt 21–319

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	7rst
Deposition date deposition_date	2021-08-11
Structure title title	The Crystal Structure of Recombinant Chloroperoxidase Expressed in Aspergillus niger
Keywords keywords	recombinant chloroperoxidase, Aspergillus niger, OXIDOREDUCTASE; OXIDOREDUCTASE
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	19.83 Å
Radius of gyration Rg (electron density) rg_electron	18.64 Å
Forward intensity I(0) i0	27973200.00
Molecular weight molecular_weight	37947.0 kDa
Excluded volume excluded_volume	45779 Å³
Envelope volume envelope_volume	50860 Å³
Hydration-shell volume shell_volume	22005 Å³
Envelope diameter envelope_diameter	63.5 Å
Shell Rg shell_rg	25.80 Å
Envelope Rg envelope_rg	19.00 Å
Shape Rg shape_rg	18.59 Å
Total Rg total_rg	19.63 Å
Total atoms total_atoms	2594
Residues n_residues	298
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	61.5 Å
Rg (real space) rg_real	19.65 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	2.7970e+07
I(0) uncertainty (real space) i0_real_error	3.3810e+05
Rg (reciprocal space) rg_reciprocal	19.68 Å
I(0) (reciprocal space) i0_reciprocal	27970000.0000
Solution quality estimate total_estimate	0.8959
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.086
Kurtosis Kurtosis kurtosis	-0.453
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5675000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Chloroperoxidase
Molecular weight formula_weight	32746.9 kDa
EC 编号 ec_number	1.11.1.10
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	3113

QEPGSGIGYPYDNNTLPYVAPGPTDSRAPCPALNALANHGYIPHDGRAISRETLQNAFLNHMGIANSVIELALTNAFVVCEYVTGSDCGDSLVNLTLLAEPHAFEHDHSFSRKDYKQGVANSNDFIDNRNFDAETFQTSLDVVAGKTHFDYADMNEIRLQRESLSNELDFPGWFTESKPIQNVESGFIFALVSDFNLPDNDENPLVRIDWWKYWFTNESFPYHLGWHPPSPAREIEFVTSASSAVLAASVTSTPSSLPSGAIGPGAEAVPLSFASTMTPFLLATNAPYYAQDPTLGPND

来源 Source

来源生物 organism	Leptoxyphium fumago
通用名 common_name	Caldariomyces fumago
NCBI Class编号 ncbi_taxonomy_id	5474
宿主生物 host_organism	Aspergillus niger

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	12

Entity 8 Entity 8 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	468

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8. Citations (1)

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Unit-cell length a length_a	58.050 Å
Unit-cell length b length_b	150.920 Å
Unit-cell length c length_c	100.850 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.690 Å
Low-resolution limit resolution_low	30.360 Å
R factor r_factor	0.1723
R_work r_work	0.1703
R_free r_free	0.2096

fit	/app/data/saxs_computation/rs/7rst/7rst.fit
pddf	/app/data/pr_computation/rs/7rst/7rst.pr.out
profile	/app/data/saxs_computation/rs/7rst/7rst.dat