SAXSdb — 6h6f

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

TcdA1

Photorhabdus luminescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	TcdB2,TccC3,TccC3 × 1 （Q8GF97,Q8GF99）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RN43_PHOLU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–2516； UniProt 1–2516 Author chain B； PDBConstruct 1–2516； UniProt 1–2516 Author chain C； PDBConstruct 1–2516； UniProt 1–2516 Author chain D； PDBConstruct 1–2516； UniProt 1–2516 Author chain E； PDBConstruct 1–2516； UniProt 1–2516

TcdB2,TccC3,TccC3

Photorhabdus luminescens

UniProt Q8GF97

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	TcdA1 × 5 （Q9RN43）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8GF97_PHOLU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1475–2334； UniProt 1–860 Author chain F； PDBConstruct 2335–2434； UniProt 861–960

TcdB2,TccC3,TccC3

Photorhabdus luminescens

UniProt Q8GF99

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	TcdA1 × 5 （Q9RN43）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8GF99_PHOLU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1–1474； UniProt 1–1474

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	6h6f
Deposition date deposition_date	2018-07-27
Structure title title	PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A
Keywords keywords	Tc, ABC, a-PFT, membrane transport, translocation, pore forming toxin, TOXIN; TOXIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

6h6f__assembly_1__model_1

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

Download this curve (.dat)

6h6f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6h6f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	99.12 Å
Rg (electron density)	101.20 Å
Total Rg	100.90 Å
Atom count	114303
Residues	14388
Excluded volume	2021800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6h6f__assembly_1__model_1`	hexameric （6）	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 (2)

Entity 1 Entity 1 polymer

Description description	TcdA1
Molecular weight formula_weight	283229.4 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	114303

MNESVKEIPDVLKSQCGFNCLTDISHSSFNEFRQQVSEHLSWSETHDLYHDAQQAQKDNRLYEARILKRANPQLQNAVHLAILAPNAELIGYNNQFSGRASQYVAPGTVSSMFSPAAYLTELYREARNLHASDSVYYLDTRRPDLKSMALSQQNMDIELSTLSLSNELLLESIKTESKLENYTKVMEMLSTFRPSGATPYHDAYENVREVIQLQDPGLEQLNASPAIAGLMHQASLLGINASISPELFNILTEEITEGNAEELYKKNFGNIEPASLAMPEYLKRYYNLSDEELSQFIGKASNFGQQEYSNNQLITPVVNSSDGTVKVYRITREYTTNAYQMDVELFPFGGENYRLDYKFKNFYNASYLSIKLNDKRELVRTEGAPQVNIEYSANITLNTADISQPFEIGLTRVLPSGSWAYAAAKFTVEEYNQYSFLLKLNKAIRLSRATELSPTILEGIVRSVNLQLDINTDVLGKVFLTKYYMQRYAIHAETALILCNAPISQRSYDNQPSQFDRLFNTPLLNGQYFSTGDEEIDLNSGSTGDWRKTILKRAFNIDDVSLFRLLKITDHDNKDGKIKNNLKNLSNLYIGKLLADIHQLTIDELDLLLIAVGEGKTNLSAISDKQLATLIRKLNTITSWLHTQKWSVFQLFIMTSTSYNKTLTPEIKNLLDTVYHGLQGFDKDKADLLHVMAPYIAATLQLSSENVAHSVLLWADKLQPGDGAMTAEKFWDWLNTKYTPGSSEAVETQEHIVQYCQALAQLEMVYHSTGINENAFRLFVTKPEMFGAATGAAPAHDALSLIMLTRFADWVNALGEKASSVLAAFEANSLTAEQLADAMNLDANLLLQASIQAQNHQHLPPVTPENAFSCWTSINTILQWVNVAQQLNVAPQGVSALVGLDYIQSMKETPTYAQWENAAGVLTAGLNSQQANTLHAFLDESRSAALSTYYIRQVAKAAAAIKSRDDLYQYLLIDNQVSAAIKTTRIAEAIASIQLYVNRALENVEENANSGVISRQFFIDWDKYNKRYSTWAGVSQLVYYPENYIDPTMRIGQTKMMDALLQSVSQSQLNADTVEDAFMSYLTSFEQVANLKVISAYHDNINNDQGLTYFIGLSETDAGEYYWRSVDHSKFNDGKFAANAWSEWHKIDCPINPYKSTIRPVIYKSRLYLLWLEQKEITKQTGNSKDGYQTETDYRYELKLAHIRYDGTWNTPITFDVNKKISELKLEKNRAPGLYCAGYQGEDTLLVMFYNQQDTLDSYKNASMQGLYIFADMASKDMTPEQSNVYRDNSYQQFDTNNVRRVNNRYAEDYEIPSSVSSRKDYGWGDYYLSMVYNGDIPTINYKAASSDLKIYISPKLRIIHNGYEGQKRNQCNLMNKYGKLGDKFIVYTSLGVNPNNSSNKLMFYPVYQYSGNTSGLNQGRLLFHRDTTYPSKVEAWIPGAKRSLTNQNAAIGDDYATDSLNKPDDLKQYIFMTDSKGTATDVSGPVEINTAISPAKVQIIVKAGGKEQTFTADKDVSIQPSPSFDEMNYQFNALEIDGSGLNFINNSASIDVTFTAFAEDGRKLGYESFSIPVTLKVSTDNALTLHHNENGAQYMQWQSYRTRLNTLFARQLVARATTGIDTILSMETQNIQEPQLGKGFYATFVIPPYNLSTHGDERWFKLYIKHVVDNNSHIIYSGQLTDTNINITLFIPLDDVPLNQDYHAKVYMTFKKSPSDGTWWGPHFVRDDKGIVTINPKSILTHFESVNVLNNISSEPMDFSGANSLYFWELFYYTPMLVAQRLLHEQNFDEANRWLKYVWSPSGYIVHGQIQNYQWNVRPLLEDTSWNSDPLDSVDPDAVAQHDPMHYKVSTFMRTLDLLIARGDHAYRQLERDTLNEAKMWYMQALHLLGDKPYLPLSTTWSDPRLDRAADITTQNAHDSAIVALRQNIPTPAPLSLRSANTLTDLFLPQINEVMMNYWQTLAQRVYNLRHNLSIDGQPLYLPIYATPADPKALLSAAVATSQGGGKLPESFMSLWRFPHMLENARGMVSQLTQFGSTLQNIIERQDAEALNALLQNQAAELILTNLSIQDKTIEELDAEKTVLEKSKAGAQSRFDSYGKLYDENINAGENQAMTLRASAAGLTTAVQASRLAGAAADLVPNIFGFAGGGSRWGAIAEATGYVMEFSANVMNTEADKISQSETYRRRRQEWEIQRNNAEAELKQIDAQLKSLAVRREAAVLQKTSLKTQQEQTQSQLAFLQRKFSNQALYNWLRGRLAAIYFQFYDLAVARCLMAEQAYRWELNDDSARFIKPGAWQGTYAGLLAGETLMLSLAQMEDAHLKRDKRALEVERTVSLAEVYAGLPKDNGPFSLAQEIDKLVSQGSGSAGSGNNNLAFGAGTDTKTSLQASVSFADLKIREDYPASLGKIRRIKQISVTLPALLGPYQDVQAILSYGDKAGLANGCEALAVSHGMNDSGQFQLDFNDGKFLPFEGIAIDQGTLTLSFPNASMPEKGKQATMLKTLNDIILHIRYTIK

Source Source

Source organism organism	Photorhabdus luminescens
Common name common_name	Xenorhabdus luminescens
NCBI taxonomy ID ncbi_taxonomy_id	29488
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TcdB2,TccC3,TccC3
Molecular weight formula_weight	273634.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MQNSQDFSITELSLPKGGGAITGMGEALTPTGPDGMAALSLPLPISAGRGYAPAFTLNYNSGAGNSPFGLGWDCNVMTIRRRTHFGVPHYDETDTFLGPEGEVLVVADQPRDESTLQGINLGATFTVTGYRSRLESHFSRLEYWQPKTTGKTDFWLIYSPDGQVHLLGKSPQARISNPSQTTQTAQWLLEASVSSRGEQIYYQYRAEDDTGCEADEITHHLQATAQRYLHIVYYGNRTASETLPGLDGSAPSQADWLFYLVFDYGERSNNLKTPPAFSTTGSWLCRQDRFSRYEYGFEIRTRRLCRQVLMYHHLQALDSKITEHNGPTLVSRLILNYDESAIASTLVFVRRVGHEQDGNVVTLPPLELAYQDFSPRHHAHWQPMDVLANFNAIQRWQLVDLKGEGLPGLLYQDKGAWWYRSAQRLGEIGSDAVTWEKMQPLSVIPSLQSNASLVDINGDGQLDWVITGPGLRGYHSQRPDGSWTRFTPLNALPVEYTHPRAQLADLMGAGLSDLVLIGPKSVRLYANTRDGFAKGKDVVQSGDITLPVPGADPRKLVAFSDVLGSGQAHLVEVSATKVTCWPNLGRGRFGQPITLPGFSQPATEFNPAQVYLADLDGSGPTDLIYVHTNRLDIFLNKSGNGFAEPVTLRFPEGLRFDHTCQLQMADVQGLGVASLILSVPHMSPHHWRCDLTNMKPWLLNEMNNNMGVHHTLRYRSSSQFWLDEKAAALTTGQTPVCYLPFPIHTLWQTETEDEISGNKLVTTLRYARGAWDGREREFRGFGYVEQTDSHQLAQGNAPERTPPALTKNWYATGLPVIDNALSTEYWRDDQAFAGFSPRFTTWQDNKDVPLTPEDDNSRYWFNRALKGQLLRSELYGLDDSTNKHVPYTVTEFRSQVRRLQHTDSRYPVLWSSVVESRNYHYERIASDPQCSQNITLSSDRFGQPLKQLSVQYPRRQQPAINLYPDTLPDKLLANSYDDQQRQLRLTYQQSSWHHLTNNTVRVLGLPDSTRSDIFTYGAENVPAGGLNLELLSDKNSLIADDKPREYLGQQKTAYTDGQNTTPLQTPTRQALIAFTETTVFNQSTLSAFNGSIPSDKLSTTLEQAGYQQTNYLFPRTGEDKVWVAHHGYTDYGTAAQFWRPQKQSNTQLTGKITLIWDANYCVVVQTRDAAGLTTSAKYDWRFLTPVQLTDINDNQHLITLDALGRPITLRFWGTENGKMTGYSSPEKASFSPPSDVNAAIELKKPLPVAQCQVYAPESWMPVLSQKTFNRLAEQDWQKLYNARIITEDGRICTLAYRRWVQSQKAIPQLISLLNNGPRLPPHSLTLTTDRYDHDPEQQIRQQVVFSDGFGRLLQAAARHEAGMARQRNEDGSLIINVQHTENRWAVTGRTEYDNKGQPIRTYQPYFLNDWRYVSNDSARQEKEAYADTHVYDPIGREIKVITAKGWFRRTLFTPWFTVNEDENDTAAEVKKVKMMKNIDPKLYQKTPTVSVYDNRGLIIRNIDFHRTTANGDPDTRITRHQYDIHGHLNQSIDPRLYEAKQTNNTIKPNFLWQYDLTGNPLCTESIDAGRTVTLNDIEGRPLLTVTATGVIQTRQYETSSLPGRLLSVAEQTPEEKTSRITERLIWAGNTEAEKDHNLAGQCVRHYDTAGVTRLESLSLTGTVLSQSSQLLIDTQEANWTGDNETVWQNMLADDIYTTLSTFDATGALLTQTDAKGNIQRLAYDVAGQLNGSWLTLKGQTEQVIIKSLTYSAAGQKLREEHGNDVITEYSYEPETQRLIGIKTRRPSDTKVLQDLRYEYDPVGNVISIRNDAEATRFWHNQKVMPENTYTYDSLYQLISATGREMANIGQQSHQFPSPALPSDNNTYTNYTRTYTYDRGGNLTKIQHSSPATQNNYTTNITVSNRSNRAVLSTLTEDPAQVDALFDAGGHQNTLISGQNLNWNTRGELQQVTLVKRDKGANDDREWYRYSGDGRRMLKINEQQASNNAQTQRVTYLPNLELRLTQNSTATTEDLQVITVGEAGRAQVRVLHWESGKPEDIDNNQLRYSYDNLIGSSQLELDSEGQIISEEEYYPYGGTALWAARNQTEASYKTIRYSGKERDATGLYYYGYRYYQPWIGRWLSSAPAGTIDGLNLYRMVRNNPVTLLDPDGLMPTIAERIAALKKNKVTDSAPSPANATNVAINIRPPVAPKPSLPKASTSSQPTTHPIGAANIKPTTSGSSIVAPLSPVGNKSTSEISLPESAQSSSSSTTSTNLQKKSFTLYRADNRSFEEMQSKFPEGFKAWTPLDTKMARQFASIFIGQKDTSNLPKETVKNISTWGAKPKLKDLSNYIKYTKDKSTVWVSTAINTEAGGQSSGAPLHKIDMDLYEFAIDGQKLNPLPEGRTKNMVPSLLLDTPQIETSSIIALNHGPVNDAEISFLTTIPLKNVKPHKR

Source Source

Source organism organism	Photorhabdus luminescens
Common name common_name	Xenorhabdus luminescens
NCBI taxonomy ID ncbi_taxonomy_id	29488
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	3.72 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	132000

PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A

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

TcdA1

State in the Current Structure

Other States of the Same Protein in the Database

TcdB2,TccC3,TccC3

State in the Current Structure

Other States of the Same Protein in the Database

TcdB2,TccC3,TccC3

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6h6f__assembly_1__model_1

6h6f__assembly_1__model_1 | I(q)

6h6f__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A

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

TcdA1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TcdB2,TccC3,TccC3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TcdB2,TccC3,TccC3

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

6h6f__assembly_1__model_1

6h6f__assembly_1__model_1 | I(q)

6h6f__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)