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- PDB-4q7k: Structure of NBD287 of TM287/288 -

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Basic information

Entry
Database: PDB / ID: 4q7k
TitleStructure of NBD287 of TM287/288
ComponentsABC transporterATP-binding cassette transporter
KeywordsMETAL BINDING PROTEIN / ABC-type 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 / membrane / metal ion binding
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-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...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-like, conserved site / ABC transporters family signature. / 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
ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter


Theoretical massNumber of molelcules
Total (without water)27,6541
Polymers27,6541
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.170, 80.170, 129.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ABC transporter / ATP-binding cassette transporter / ABC transporter / ATP-binding protein / Lipid A export ATP-binding/permease protein MsbA


Mass: 27653.572 Da / Num. of mol.: 1 / Fragment: unp residues 330-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0287, THEMA_03290, Tmari_0285 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 100 mM Tris-HCl, 100 mM sodium acetate, 25 % PEG2000 MME, pH 7.8, VAPOR DIFFUSION, HANGING 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: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2012
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.367 Å / Num. all: 23512 / Num. obs: 23505 / % possible obs: 99.97 % / 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: 1.8→47.367 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 1175 5 %random
Rwork0.2042 ---
obs0.2046 23505 99.97 %-
all-23512 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→47.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 0 61 1524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071486
X-RAY DIFFRACTIONf_angle_d1.1262001
X-RAY DIFFRACTIONf_dihedral_angle_d14.591562
X-RAY DIFFRACTIONf_chiral_restr0.047233
X-RAY DIFFRACTIONf_plane_restr0.004253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.88190.31821440.28692724X-RAY DIFFRACTION100
1.8819-1.98120.29011430.25752719X-RAY DIFFRACTION100
1.9812-2.10530.28091440.22212750X-RAY DIFFRACTION100
2.1053-2.26780.22221440.21232733X-RAY DIFFRACTION100
2.2678-2.49610.21741460.21132771X-RAY DIFFRACTION100
2.4961-2.85720.25631470.21912784X-RAY DIFFRACTION100
2.8572-3.59960.21461490.21512833X-RAY DIFFRACTION100
3.5996-47.38310.18421580.18573016X-RAY DIFFRACTION100
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)
11.195-0.5841.65263.2358-1.60013.8503-0.38180.40031.3802-1.72830.16931.0789-0.449-0.46970.11720.9729-0.209-0.30210.72830.09270.916917.544739.1185-10.629
25.12741.5916-0.68025.9344-0.61433.24090.0896-0.34420.6290.226-0.05780.6801-0.7199-0.2034-0.06080.47780.0593-0.00370.366-0.04280.47733.72121.3232-0.8081
34.6582-0.29081.20772.2442-0.73622.301-0.3590.47560.090.06880.16820.3953-0.415-0.24870.20810.42620.0682-0.05160.3584-0.03710.3496.051816.584-11.815
43.8710.3870.75553.47470.16343.67830.0202-0.06050.07930.10890.01480.0647-0.230.286-0.02510.3676-0.0123-0.05140.2939-0.03210.310112.965319.0452-0.8801
54.29181.64780.62212.7583-0.24142.6807-0.25870.2350.6525-0.36430.49150.4160.2541-0.0596-0.22990.5131-0.1172-0.08730.5376-0.03770.531725.486538.3077-4.3632
64.76530.6156-0.01813.9723-0.26666.37260.018-0.60360.54080.67830.2402-0.63930.2160.718-0.1840.5302-0.09180.00790.6561-0.17590.552131.882342.16985.6328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 353:409)
2X-RAY DIFFRACTION2(chain A and resid 410:428)
3X-RAY DIFFRACTION3(chain A and resid 429:442)
4X-RAY DIFFRACTION4(chain A and resid 443:515)
5X-RAY DIFFRACTION5(chain A and resid 516:558)
6X-RAY DIFFRACTION6(chain A and resid 559:570)

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