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- PDB-4q7l: Structure of NBD288 of TM287/288 -

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Basic information

Entry
Database: PDB / ID: 4q7l
TitleStructure of NBD288 of TM287/288
ComponentsUncharacterized ABC transporter ATP-binding protein TM_0288
KeywordsMETAL BINDING PROTEIN / ABC-tpye Nucleotide Binding Domain (NBD)
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Uncharacterized ABC transporter ATP-binding protein TM_0288
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBukowska, M.A. / Hohl, M. / Gruetter, M.G. / Seeger, M.A.
CitationJournal: Biochemistry / Year: 2015
Title: A Transporter Motor Taken Apart: Flexibility in the Nucleotide Binding Domains of a Heterodimeric ABC Exporter.
Authors: Bukowska, M.A. / Hohl, M. / Geertsma, E.R. / Hurlimann, L.M. / Grutter, M.G. / Seeger, M.A.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized ABC transporter ATP-binding protein TM_0288
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
C: Uncharacterized ABC transporter ATP-binding protein TM_0288
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6944
Polymers86,6353
Non-polymers591
Water3,927218
1
A: Uncharacterized ABC transporter ATP-binding protein TM_0288


Theoretical massNumber of molelcules
Total (without water)28,8781
Polymers28,8781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9372
Polymers28,8781
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized ABC transporter ATP-binding protein TM_0288


Theoretical massNumber of molelcules
Total (without water)28,8781
Polymers28,8781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.930, 95.930, 88.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Uncharacterized ABC transporter ATP-binding protein TM_0288


Mass: 28878.289 Da / Num. of mol.: 3 / Fragment: unp residues 353-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0288 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC4
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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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: 54.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-HAOAc pH 7.5, 200 mM MgCl2, 8 % PEG550 MME, 8 % PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2013
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→47.965 Å / Num. all: 37961 / Num. obs: 37661 / % possible obs: 99.21 % / Observed criterion σ(F): -3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.9_1678)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→47.965 Å / SU ML: 0.36 / σ(F): 1.98 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1885 5.01 %random
Rwork0.1931 ---
obs0.1952 37661 99.21 %-
all-37961 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→47.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 1 218 6117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046049
X-RAY DIFFRACTIONf_angle_d0.8538156
X-RAY DIFFRACTIONf_dihedral_angle_d15.552287
X-RAY DIFFRACTIONf_chiral_restr0.033943
X-RAY DIFFRACTIONf_plane_restr0.0031028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.41360.34911470.28862785X-RAY DIFFRACTION99
2.4136-2.48460.31981430.25622717X-RAY DIFFRACTION99
2.4846-2.56480.34671460.24542776X-RAY DIFFRACTION100
2.5648-2.65650.2921450.23762756X-RAY DIFFRACTION100
2.6565-2.76280.29131460.23412779X-RAY DIFFRACTION99
2.7628-2.88850.30671440.23712742X-RAY DIFFRACTION99
2.8885-3.04080.28991460.23012758X-RAY DIFFRACTION100
3.0408-3.23130.2641440.21462753X-RAY DIFFRACTION100
3.2313-3.48070.2411460.21172768X-RAY DIFFRACTION100
3.4807-3.83090.27731420.2052685X-RAY DIFFRACTION96
3.8309-4.38490.20061440.16662738X-RAY DIFFRACTION99
4.3849-5.52320.16191460.13932762X-RAY DIFFRACTION100
5.5232-47.9750.17931460.15312757X-RAY DIFFRACTION99
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)
13.5027-0.06330.13752.6712-0.01663.39860.0751-0.08150.0531-0.0953-0.13290.2038-0.4612-0.20120.02750.29440.0498-0.00050.2336-0.0260.2351-51.472698.8375-8.3166
28.1196-1.8516-0.79554.62481.1644.75520.49751.1250.0232-0.2956-0.0618-0.3532-0.31370.1052-0.34170.42930.09260.06550.54590.00350.4831-29.002889.0468-25.9915
37.408-2.7182-2.05933.37791.38034.28210.0881-0.3409-0.47410.25950.1183-0.52170.53510.7734-0.18310.4490.1071-0.04020.39320.00860.4589-32.074991.0307-12.1837
43.447-1.10411.4475.0745-2.35164.5389-0.0839-0.1449-0.24790.01770.1522-0.22570.1881-0.04940.00340.2967-0.0185-0.02460.29250.00880.2275-42.251584.26143.8737
53.63071.1828-1.97363.39420.24135.2453-0.1919-0.5092-0.26730.0294-0.0681-0.24770.17250.10010.24570.50.0305-0.00480.47220.01680.3654-8.820198.91624.7058
61.54-0.2704-0.8627.7384-3.38542.1202-0.1804-0.07940.5701-0.50040.3652-0.01190.0939-0.1793-0.14340.5227-0.0181-0.11780.5654-0.11910.6093-16.519117.67389.9973
72.56331.1083-0.16383.38091.48325.2996-0.06850.0033-0.1496-0.0131-0.03410.0738-0.32240.33620.18290.44180.0144-0.0160.5488-0.06490.41-6.1295112.961535.4241
83.59043.6595-0.05644.25960.41322.0631-0.16580.97130.65820.01280.21770.2865-0.27590.80430.55140.9532-0.18390.19171.11660.04251.1092.8954123.020328.3658
92.55070.70820.05335.4444-1.98993.32980.02650.0519-0.1490.0271-0.3761-0.40610.09510.57890.28390.2741-0.02180.03920.44090.09640.314-31.37135.5605-33.1989
105.91321.51963.32454.88420.76645.8655-0.02460.7351-0.8073-0.41830.2350.33550.16670.7463-0.21230.4816-0.00220.07920.5475-0.02720.556-48.6856121.9808-52.0568
114.48212.81882.91814.08650.414.26330.1542-0.5478-0.46370.21470.12060.62890.2334-0.6789-0.32720.46210.03050.08520.54030.04050.6063-47.2106121.0694-38.4833
124.37260.9732-1.63114.7513-0.93344.6270.1274-0.38860.02480.0836-0.11810.1278-0.1513-0.10440.14410.3563-0.0190.00710.39910.03990.2651-46.3149131.8934-20.2868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 352:435)
2X-RAY DIFFRACTION2(chain A and resid 436:501)
3X-RAY DIFFRACTION3(chain A and resid 502:544)
4X-RAY DIFFRACTION4(chain A and resid 545:605)
5X-RAY DIFFRACTION5(chain B and resid 352:413)
6X-RAY DIFFRACTION6(chain B and resid 414:542)
7X-RAY DIFFRACTION7(chain B and resid 543:591)
8X-RAY DIFFRACTION8(chain B and resid 592:605)
9X-RAY DIFFRACTION9(chain C and resid 352:427)
10X-RAY DIFFRACTION10(chain C and resid 428:502)
11X-RAY DIFFRACTION11(chain C and resid 503:543)
12X-RAY DIFFRACTION12(chain C and resid 544:593)

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