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- PDB-7x0q: Crystal structure of ATPase Clo1313_2554 from Clostridium thermocellum -

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Basic information

Entry
Database: PDB / ID: 7x0q
TitleCrystal structure of ATPase Clo1313_2554 from Clostridium thermocellum
ComponentsABC transporter related protein
KeywordsSUGAR BINDING PROTEIN / ABC-transporter / substrate binding protein / cellodextrin
Function / homology
Function and homology information


carbohydrate transport / ABC-type transporter activity / ATP binding
Similarity search - Function
Transport-associated OB, type 1 / TOBE domain / MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / Molybdate/tungstate binding, C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...Transport-associated OB, type 1 / TOBE domain / MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / Molybdate/tungstate binding, C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter related protein
Similarity search - Component
Biological speciesAcetivibrio thermocellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDong, S. / Yao, X. / Feng, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070125 China
National Natural Science Foundation of China (NSFC)32170051 China
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: Mbio / Year: 2022
Title: Deciphering Cellodextrin and Glucose Uptake in Clostridium thermocellum.
Authors: Yan, F. / Dong, S. / Liu, Y.J. / Yao, X. / Chen, C. / Xiao, Y. / Bayer, E.A. / Shoham, Y. / You, C. / Cui, Q. / Feng, Y.
History
DepositionFeb 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter related protein
B: ABC transporter related protein


Theoretical massNumber of molelcules
Total (without water)84,2482
Polymers84,2482
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-5 kcal/mol
Surface area33570 Å2
Unit cell
Length a, b, c (Å)104.390, 104.390, 167.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 11 or (resid 12...
21(chain B and (resid 3 through 57 or (resid 58...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYS(chain A and (resid 3 through 11 or (resid 12...AA3 - 113 - 11
12ARGARGARGARG(chain A and (resid 3 through 11 or (resid 12...AA1212
13SERSERMETMET(chain A and (resid 3 through 11 or (resid 12...AA3 - 3693 - 369
14SERSERMETMET(chain A and (resid 3 through 11 or (resid 12...AA3 - 3693 - 369
15SERSERMETMET(chain A and (resid 3 through 11 or (resid 12...AA3 - 3693 - 369
21SERSERTHRTHR(chain B and (resid 3 through 57 or (resid 58...BB3 - 573 - 57
22GLUGLUGLUGLU(chain B and (resid 3 through 57 or (resid 58...BB5858
23SERSERMETMET(chain B and (resid 3 through 57 or (resid 58...BB3 - 3693 - 369
24SERSERMETMET(chain B and (resid 3 through 57 or (resid 58...BB3 - 3693 - 369
25SERSERMETMET(chain B and (resid 3 through 57 or (resid 58...BB3 - 3693 - 369

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Components

#1: Protein ABC transporter related protein / NBD2554


Mass: 42123.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus (bacteria)
Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_1862 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3DGK4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 100 mM acetate/acetic acid pH 4.4, 200 mM Li2SO4, 2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→36.907 Å / Num. obs: 39211 / % possible obs: 100 % / Redundancy: 6.874 % / Biso Wilson estimate: 86.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.073 / Χ2: 0.96 / Net I/σ(I): 16.74 / Num. measured all: 269550 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.987.1480.6172.8520436285928590.8950.665100
2.98-3.067.1030.453.8720299285828580.9460.485100
3.06-3.156.9530.3544.8519127275127510.9610.383100
3.15-3.246.6760.285.9617845267326730.9750.304100
3.24-3.356.880.198.7517903260226020.9850.205100
3.35-3.477.2340.14311.3818084250025000.9930.154100
3.47-3.67.2150.11714.1117416241424140.9950.126100
3.6-3.747.1050.09317.3316441231423140.9960.101100
3.74-3.916.9240.07820.3515344221622160.9960.085100
3.91-4.16.5080.07222.2813998215121510.9970.078100
4.1-4.326.770.06424.6413743203020300.9970.069100
4.32-4.596.980.05927.2113450192719270.9980.064100
4.59-4.96.8470.05728.4312195178217810.9980.06199.9
4.9-5.296.7080.05627.6911390169816980.9980.061100
5.29-5.86.3190.05727.39744154215420.9960.062100
5.8-6.486.9210.05428.99634139213920.9980.058100
6.48-7.496.7460.052308331123512350.9980.056100
7.49-9.176.2630.04630.716445102910290.9980.05100
9.17-12.976.4440.04332.3652008078070.9990.046100
12.97-36.9075.8450.04628.5825254414320.9980.05198

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D62

2d62


Resolution: 2.9→36.907 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2758 1982 9.41 %
Rwork0.2231 19083 -
obs0.2281 21065 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.54 Å2 / Biso mean: 101.4855 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.9→36.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 0 0 5594
Num. residues----719
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2152X-RAY DIFFRACTION11.015TORSIONAL
12B2152X-RAY DIFFRACTION11.015TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9002-2.97270.371280.32127497
2.9727-3.0530.44561400.3041132197
3.053-3.14280.38251370.3093133499
3.1428-3.24420.37251380.2992133299
3.2442-3.36010.32141400.27641345100
3.3601-3.49450.33211400.25781342100
3.4945-3.65340.32341410.24531346100
3.6534-3.84590.29491420.22911358100
3.8459-4.08650.28251420.21251371100
4.0865-4.40160.27811430.19161379100
4.4016-4.84370.20521420.17741367100
4.8437-5.54250.23551470.19951400100
5.5425-6.97530.25831480.24151422100
6.9753-36.90.25511540.2092149299
Refinement TLS params.

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

IDL11 (°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)
12.7112.32320.00454.33251.58932.1592-0.47680.5875-0.53870.37950.01661.16950.8378-1.27050.4020.8185-0.44490.32621.1049-0.39291.1239-41.8419-25.99543.0109
24.7679-2.60521.57074.87063.44878.5025-0.4131.2969-0.5272-1.01510.6862-1.1211-0.24081.2991-0.06010.8357-0.29740.23611.1446-0.09050.9826-24.983-13.0994-14.262
39.20432.1136-7.25488.1188-1.58925.70640.27750.03610.21811.049-0.30270.3067-0.3479-0.15490.1920.6548-0.19160.08110.6859-0.08980.331-31.6528-10.79030.989
43.59670.10040.59261.38440.19246.6498-0.23740.1540.05850.19850.2316-0.43150.0024-0.12540.02010.7656-0.05560.15210.4408-0.10250.6728-29.4989-9.92132.3827
53.17231.0996-0.66664.0423-0.04824.0004-0.0328-0.06130.73270.50680.4017-1.0487-0.12260.4149-0.33220.55610.05730.0150.5108-0.30271.435511.002311.893911.6097
65.741-3.7224-6.21368.31264.18616.7895-0.32850.73150.38771.4572-0.3144-2.26150.4460.34290.69650.7421-0.0638-0.1370.5227-0.01541.190514.7061-11.51174.9814
76.6939-0.7034.42581.98711.38856.71690.25520.1391-0.05061.07730.3238-0.6790.670.3133-0.42110.89690.0042-0.07180.5359-0.23841.31256.4674-16.66258.0325
88.54058.084.24669.36130.78148.8021-0.3217-0.2682-0.24160.83570.29960.58150.183-0.94590.11740.76940.05690.10420.5464-0.25781.0863-0.0546-2.890514.2357
95.41310.0038-1.0651.2860.50882.4539-0.031-0.23241.01640.03050.3266-0.3122-0.1353-0.1664-0.22360.52430.03970.01130.4431-0.07020.9076-22.423617.168120.9013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 81 )B3 - 81
2X-RAY DIFFRACTION2chain 'B' and (resid 82 through 149 )B82 - 149
3X-RAY DIFFRACTION3chain 'B' and (resid 150 through 201 )B150 - 201
4X-RAY DIFFRACTION4chain 'B' and (resid 202 through 369 )B202 - 369
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 77 )A3 - 77
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 110 )A78 - 110
7X-RAY DIFFRACTION7chain 'A' and (resid 111 through 150 )A111 - 150
8X-RAY DIFFRACTION8chain 'A' and (resid 151 through 201 )A151 - 201
9X-RAY DIFFRACTION9chain 'A' and (resid 202 through 369 )A202 - 369

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