2ynm

Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a

Method: X-RAY DIFFRACTION

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

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN

PROCHLOROCOCCUS MARINUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N × 2 （Q7VD37） LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B × 2 （Q7VD38） PENTAETHYLENE GLYCOL × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 8 ALUMINUM FLUORIDE × 4 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4 IRON/SULFUR CLUSTER × 4 GLYCEROL × 8 Protochlorophyllide × 2 POTASSIUM ION × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHLL_PROMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–301； UniProt 1–296 Author chain B； PDBConstruct 6–301； UniProt 1–296

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N

PROCHLOROCOCCUS MARINUS

UniProt Q7VD37

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN × 4 （Q7VD39） LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B × 2 （Q7VD38） PENTAETHYLENE GLYCOL × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 8 ALUMINUM FLUORIDE × 4 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4 IRON/SULFUR CLUSTER × 4 GLYCEROL × 8 Protochlorophyllide × 2 POTASSIUM ION × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHLN_PROMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 9–426； UniProt 1–418

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B

PROCHLOROCOCCUS MARINUS

UniProt Q7VD38

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN × 4 （Q7VD39） LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N × 2 （Q7VD37） PENTAETHYLENE GLYCOL × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 8 ALUMINUM FLUORIDE × 4 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4 IRON/SULFUR CLUSTER × 4 GLYCEROL × 8 Protochlorophyllide × 2 POTASSIUM ION × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CHLB_PROMA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–530； UniProt 1–530

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	2ynm
Deposition date deposition_date	2012-10-16
Structure title title	Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a
Keywords keywords	IRON-SULFUR CLUSTER, OXIDOREDUCTASE, METALLOENZYME, ELECTRON TRANSFER, CHLOROPHYLL SYNTHESIS, ATPASE, DYNAMIC SWITCH; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2ynm__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ynm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ynm__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	51.44 Å
Rg (electron density)	51.56 Å
Total Rg	51.68 Å
Atom count	22842
Residues	2880
Excluded volume	408720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ynm__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Description description	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN
Molecular weight formula_weight	32845.4 kDa
EC 编号 ec_number	1.3.7.7, 1.18.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11825

GPLGSMTTTLANRPDGEGSVQVKLDPKVNIEEGALVIAVYGKGGIGKSTTSSNLSAAFSKLGKKVLQIGCDPKHDSTFTLTHKMVPTVIDILEEVDFHSEELRPQDFMFEGFNGVQCVESGGPPAGTGCGGYVTGQTVKLLKEHHLLEDTDVVIFDVLGDVVCGGFAAPLQHANYCLIVTANDFDSIFAMNRIVAAINAKAKNYKVRLGGVIANRSAELDQIEKFNEKTGLKTMAHFRNVDAIRRSRLKKCTIFEMDPEEEGVLEVQNEYLSLAKKMIDNVEPLEAEPLKDREIFDLLGFD

Source Source

Source organism organism	PROCHLOROCOCCUS MARINUS
NCBI taxonomy ID ncbi_taxonomy_id	1219
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N
Molecular weight formula_weight	47040.3 kDa
EC 编号 ec_number	1.3.7.7, 1.18.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPLGSPEFMSGSTLLKETGPREVFCGLTSIVWLHRRMPDAFFLVVGSRTCAHLIQSAAGVMIFAEPRFGTAILEERDLAGLADAHEELDRVVKSLLKRRPEIRTLFLVGSCPSEVIKIDLSRAAERLSSQFNGQVRILNYSGSGIETTFTQGEDGALKALVPLMPSSQEEQLLLAGTLANPVEDRLKTIFNRLGIQKVESFPPRESTKLPAIGPGTKVLLAQPYLTDTARELKDRGAEILQAPFPLGVEGSQLWIEAAANAFKIKKTLVDATLEPLITRAHKALKPYVEQLSGKKLFLLPESQLEIPLARFLSNECGMKLIEVGVPYLNREMMGPELDLLPQNTRIVEGQHVEKQLDRVREHHPDLVVCGMGLANPLEAEGISTKWSIEMVFSPIHGIDQASDLAELFARPLHRQNLLNKKTLEAV

Source Source

Source organism organism	PROCHLOROCOCCUS MARINUS
NCBI taxonomy ID ncbi_taxonomy_id	1219
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B
Molecular weight formula_weight	58798.5 kDa
EC 编号 ec_number	1.3.7.7, 1.18.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MELTLWTYEGPPHIGAMRIATSMKGLHYVLHAPQGDTYADLLFTMIERRGSRPPVTYTTFQARDLGGDTAELVKGHIFEAVERFKPEALLVGESCTAELIQDQPGSLAKGMGLNIPIVSLELPAYSKKENWGASETFYQLIRGLLKEISEDSSNNAKQSWQEEGRRPRVNLLGPSLLGFRCRDDVLEIQKILGENGIDINVIAPLGASPSDLMRLPKADANVCLYPEIAESTCLWLERNFKTPFTKVVPIGVKATQDFLEELYELLGMEVSNSISNSDQSKLPWYSKSVDSNYLTGKRVFIFGDGTHVLAAARIANEELGFEVVGIGTYSREMARKVRAAATELGLEALITNDYLEVEESIKECAPELVLGTQMERHSAKRLGIPCAVISTPMHVQDVPARYSPQMGWEGANVIFDDWVHPLMMGLEEHLIGMFRHDFEFTDGHQSHLGHLGGHASETKTSSKGINQSPNNHSPAGESIHWTSEGESELAKIPFFVRGKVRRNTEKYARQAGCREIDGETLLDAKAHFGA

Source Source

Source organism organism	PROCHLOROCOCCUS MARINUS
NCBI taxonomy ID ncbi_taxonomy_id	1219
Host organism host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	Protochlorophyllide
Molecular weight formula_weight	613.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	382

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ynma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d2ynmb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

CATH v4.4 (9 domains)

Domain ID domain_id	2ynmA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2ynmB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2ynmC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2ynmC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2ynmC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2ynmD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2ynmD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2ynmD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1980 — Nitrogenase molybdenum iron protein domain

Domain ID domain_id	2ynmD04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	550 — Proto-chlorophyllide reductase 57 kD subunit B

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Unit-cell length a length_a	308.400 Å
Unit-cell length b length_b	74.110 Å
Unit-cell length c length_c	74.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	34.510 Å
R factor r_factor	0.2006
R_work r_work	0.1989
R_free r_free	0.2331

Structure of the ADPxAlF3-Stabilized Transition State of the Nitrogenase-like Dark-Operative Protochlorophyllide Oxidoreductase Complex from Prochlorococcus marinus with Its Substrate Protochlorophyllide a

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

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE IRON-SULFUR ATP-BINDING PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ynm__assembly_1__model_1

2ynm__assembly_1__model_1 | I(q)

2ynm__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source 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 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (2 domains)

CATH v4.4 (9 domains)

7. Citations (1)