PDB-9pmy: Crystal Structure of an ATP-Binding Cassette (ABC) Transporter As...

ID or keywords:

Entry

Database: PDB / ID: 9pmy

Title

Crystal Structure of an ATP-Binding Cassette (ABC) Transporter Associated, Xyloglucan-Binding Protein from the Extremely Thermophilic, Lignocellulose Degrading Bacterium Anaerocellum (f. Caldicellulosiruptor) bescii

Components

Extracellular solute-binding protein family 1

Keywords

SUGAR BINDING PROTEIN / XYLOGLUCAN / ABC SUBSTRATE BINDING / THERMOPHILE

Function / homology

: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / PHOSPHATE ION / Extracellular solute-binding protein family 1

Function and homology information

Biological species

Caldicellulosiruptor bescii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.43 Å

Authors

Tjo, H. / Jeffrey, P.D. / Conway, J.M.

Funding support

1items

Citation

Journal: Febs J. / Year: 2026
Title: Structural insights into xyloglucan recognition by an ABC transporter from a Gram-positive, thermophilic bacterium.
Authors: Tjo, H. / Jiang, V. / Jeffrey, P.D. / Zhu, A. / Link, A.J. / Joseph, J.A. / Conway, J.M.

History

Deposition	Jul 18, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release
Revision 1.1	Aug 26, 2026	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9pmy.cif.gz	540.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9pmy.ent.gz	371.9 KB	Display	PDB format
PDBx/mmJSON format	9pmy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pm/9pmy ftp://data.pdbj.org/pub/pdb/validation_reports/pm/9pmy	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (1)

Deposited unit

A: Extracellular solute-binding protein family 1

B: Extracellular solute-binding protein family 1

hetero molecules

126 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Extracellular solute-binding protein family 1

hetero molecules

defined by author
Evidence: gel filtration
63.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Extracellular solute-binding protein family 1

defined by author
Evidence: gel filtration
63 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.291, 129.997, 111.249
Angle α, β, γ (deg.)	90.000, 93.611, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Extracellular solute-binding protein family 1 Mass: 63046.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor bescii (bacteria) / Gene: Athe_2052 / Production host: Escherichia coli (E. coli) / References: UniProt: B9MLD9
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.36 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 8000, Potassium Phosphate, Tris, NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9201 Å / Relative weight: 1
Reflection	Resolution: 2.43→29.84 Å / Num. obs: 46233 / % possible obs: 99.6 % / Redundancy: 4.7 % / B_iso Wilson estimate: 51.51 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.095 / R_pim(I) all: 0.049 / R_rim(I) all: 0.107 / Χ²: 0.95 / Net I/σ(I): 10.4 / Num. measured all: 219243
Reflection shell	Resolution: 2.43→2.49 Å / % possible obs: 97.4 % / Redundancy: 4.4 % / R_merge(I) obs: 0.775 / Num. measured all: 14799 / Num. unique obs: 3328 / CC_1/2: 0.679 / R_pim(I) all: 0.411 / R_rim(I) all: 0.88 / Χ²: 0.73 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	1.17_3644	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.43→29.84 Å / SU ML: 0.2835 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.2836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2179	2267	4.91 %
R_work	0.1641	43931	-
obs	0.1668	46198	99.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 69.56 Å²

Refinement step

Cycle: LAST / Resolution: 2.43→29.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8621	0	10	329	8960

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075	8895
X-RAY DIFFRACTION	f_angle_d	0.9147	12085
X-RAY DIFFRACTION	f_chiral_restr	0.0542	1299
X-RAY DIFFRACTION	f_plane_restr	0.0068	1528
X-RAY DIFFRACTION	f_dihedral_angle_d	19.3207	3350

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.43-2.48	0.293	125	0.2359	2697	X-RAY DIFFRACTION	97.04
2.48-2.54	0.2672	151	0.2162	2739	X-RAY DIFFRACTION	99.86
2.54-2.6	0.2577	143	0.2064	2711	X-RAY DIFFRACTION	99.86
2.6-2.67	0.2733	159	0.1925	2722	X-RAY DIFFRACTION	99.86
2.67-2.75	0.2461	152	0.1838	2709	X-RAY DIFFRACTION	99.97
2.75-2.84	0.2628	120	0.1818	2777	X-RAY DIFFRACTION	99.83
2.84-2.94	0.303	117	0.1948	2781	X-RAY DIFFRACTION	99.79
2.94-3.06	0.257	126	0.185	2769	X-RAY DIFFRACTION	99.93
3.06-3.2	0.2482	141	0.1861	2723	X-RAY DIFFRACTION	99.83
3.2-3.37	0.2333	138	0.1882	2771	X-RAY DIFFRACTION	99.9
3.37-3.58	0.235	162	0.1726	2718	X-RAY DIFFRACTION	99.83
3.58-3.85	0.186	154	0.154	2739	X-RAY DIFFRACTION	99.9
3.85-4.24	0.2271	162	0.1496	2730	X-RAY DIFFRACTION	99.69
4.24-4.85	0.1867	127	0.1305	2805	X-RAY DIFFRACTION	99.83
4.85-6.1	0.183	146	0.1548	2747	X-RAY DIFFRACTION	99.79
6.1-29.84	0.1908	144	0.1495	2793	X-RAY DIFFRACTION	99.63

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.94775162742	-0.856830516191	0.327528456839	4.38791215306	-1.21555090883	4.38956046409	0.198428014973	0.372990656504	0.0654123176674	-0.0688610322189	-0.288299638258	-0.361608436542	0.116352078696	0.405257899757	0.111955487543	0.415134699911	0.0726091395979	-0.0285121016078	0.370892473871	-0.0576390730227	0.383035052061	1.54939896588	5.45512460408	-22.3540809599
2	1.99030169269	-0.233031030905	0.0141334139361	4.02572042841	4.6486889774	7.3286404235	0.376776724787	0.307690096371	-0.0696314755555	-0.347268593256	-0.159820361126	0.159077105762	-0.279917877333	-0.335187890921	-0.206685418066	0.517663168347	0.0510550454055	-0.0933798369801	0.338950166884	0.0109973124697	0.444240529208	-13.8556580152	14.8026963127	-20.0443761856
3	1.50993369541	-0.604241251611	2.10701230414	1.35722767691	-0.579020869591	4.79232327392	-0.0841411462268	-0.0578917912543	0.149589173967	-0.151478946757	-0.0945185238489	0.0904047989836	-0.469604509535	-0.249829445787	0.190762878848	0.380998852558	0.0313094982237	0.0583346142376	0.311820158876	-0.020282018584	0.370997806264	-13.7066289986	41.9149032053	2.0063369149
4	0.55381548168	-0.188313854533	0.0755385615715	1.77841083992	1.24335523728	1.11194580986	0.206925819826	-0.0346936205216	-0.14768332141	0.0880076543904	-0.0442274853839	0.00958572939854	0.327692594164	-0.0483938226533	-0.162819280413	0.436420072511	-0.0304318215186	-0.0366906631993	0.324947082138	0.00653916654963	0.363133751466	-7.78858186581	12.9486248977	-2.4868600493
5	1.24804441644	-0.0244839716667	0.663646758636	5.00058664634	1.61938001847	5.64545657535	0.0998851024745	0.0632345548186	-0.0703662807587	-1.0756799968	-0.19384757451	0.0442368337997	-0.1932607358	-0.249011382972	0.0794264579865	0.338429279773	0.109903126371	-0.0178879653621	0.377831625	0.0391212031696	0.413895243788	-15.2321696996	37.4742329685	-16.2458360094
6	0.897697199456	-1.4959103557	-0.669333912509	7.55051860602	1.65296861021	2.06664022393	0.155075644494	0.105146070085	0.128294596827	-1.18529978746	-0.327596665778	0.542131336253	-0.872829494452	-0.374483610869	0.246907819169	0.632215283669	0.173467833332	-0.0920593931784	0.491919253198	0.0242050100156	0.459938766156	-21.0724143195	42.7738500196	-20.099809935
7	1.33061271083	0.397184098542	-0.71202157402	4.65093196684	-1.84464570245	3.84532571067	-0.330898140575	-0.509164939112	-0.449285019597	0.790750925226	0.623325250687	1.19002870792	0.0627250227585	-0.544013420842	-0.236688563184	0.821849721856	0.241454660408	0.218836002568	0.842096126338	0.385397174526	1.02559044094	-4.09933993825	-1.59604228849	53.6972864421
8	3.28173069818	-1.14432532586	2.03672576721	2.59542556536	-0.458246489792	5.51486810696	-0.458872387511	-0.279756612009	0.372598398126	0.567475748523	0.0678165395906	-0.495349809479	-0.27159359384	0.351118187281	0.375818583712	0.375446810787	-0.00744450722216	-0.0652231017658	0.407339486032	-0.0226203904514	0.473794558977	8.38491791225	35.3914117795	39.2649842537
9	0.444279581914	-1.45743614708	0.931909515977	4.08555167578	-2.1490997591	2.6737042949	-0.0155939615555	-0.333625879279	-0.513598501318	-0.17765718777	0.490374969919	0.634965571464	0.767733827981	-0.181269807806	-0.34891601361	0.627576983077	0.0500550565689	0.0516544257404	0.562260332413	0.171735417528	0.615871369805	1.1304374011	7.55454931465	35.9927261723
10	2.27000124278	-1.62561237471	0.896383624614	4.92871539137	-0.709000342379	3.67773977627	-0.634398237419	-1.0743688436	0.262158863884	1.39299248157	0.31138037833	-0.609753512238	-0.102002548755	0.292091862186	0.298723847096	0.993991630497	0.253126838859	-0.225766944472	1.12043292173	-0.0830140237763	0.632696187541	13.475609269	28.6128241389	59.3131729791

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 33 through 134 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 135 through 174 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 175 through 322 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 323 through 478 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 479 through 523 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 524 through 565 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 33 through 174 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 175 through 322 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 323 through 484 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 485 through 565 )

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