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- PDB-2pcl: Crystal structure of ABC transporter with complex (aq_297) from a... -

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Basic information

Entry
Database: PDB / ID: 2pcl
TitleCrystal structure of ABC transporter with complex (aq_297) from aquifex aeolicus VF5
ComponentsLipoprotein-releasing system ATP-binding protein lolD
KeywordsHYDROLASE / ABC transporter / ATP-binding protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Lipoprotein release ATP-binding protein lolD family profile. / MacB, ATP-binding domain / 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 ...Lipoprotein release ATP-binding protein lolD family profile. / MacB, ATP-binding domain / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipoprotein-releasing system ATP-binding protein LolD
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJeyakanthan, J. / Kanaujia, S.P. / Rafi, Z.A. / Sekar, K. / Ebihara, A. / Nakagawa, N. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of ABC transporter with complex (aq_297) from aquifex aeolicus VF5
Authors: Jeyakanthan, J. / Kanaujia, S.P. / Rafi, Z.A. / Sekar, K. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S.
History
DepositionMar 30, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein-releasing system ATP-binding protein lolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,83413
Polymers24,9231
Non-polymers91112
Water5,945330
1
A: Lipoprotein-releasing system ATP-binding protein lolD
hetero molecules

A: Lipoprotein-releasing system ATP-binding protein lolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66826
Polymers49,8462
Non-polymers1,82224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area5490 Å2
ΔGint-144 kcal/mol
Surface area20550 Å2
MethodPISA, PQS
2
A: Lipoprotein-releasing system ATP-binding protein lolD
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)155,00478
Polymers149,5386
Non-polymers5,46672
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
crystal symmetry operation12_345-x-4/3,-x+y-2/3,-z+1/31
Buried area20140 Å2
ΔGint-533 kcal/mol
Surface area59090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.177, 104.177, 135.046
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-230-

SO4

21A-473-

HOH

31A-478-

HOH

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Components

#1: Protein Lipoprotein-releasing system ATP-binding protein lolD / ABC transporter


Mass: 24923.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CONDON PLUS (DE3)-RIL
References: UniProt: O66646, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.075M Sodium Acetate trihydrate, 1.5M Ammonium Sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 15, 2006 / Details: RH Coated Bent-Cyrindrical MIRROR
RadiationMonochromator: SI 1 1 1 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 31017 / % possible obs: 99.7 % / Rmerge(I) obs: 0.031 / Rsym value: 0.037
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.249 / Num. unique all: 3058 / Rsym value: 0.276 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3O

1f3o


Resolution: 1.7→42.8 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.336 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24694 1567 5.1 %RANDOM
Rwork0.20096 ---
obs0.2033 29448 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.163 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 51 330 2121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221802
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.0292413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.415222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12324.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12815354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1811512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021267
X-RAY DIFFRACTIONr_nbd_refined0.2070.2835
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.223
X-RAY DIFFRACTIONr_mcbond_it1.2551.51140
X-RAY DIFFRACTIONr_mcangle_it1.80321770
X-RAY DIFFRACTIONr_scbond_it3.1493733
X-RAY DIFFRACTIONr_scangle_it4.8724.5643
LS refinement shellResolution: 1.701→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 121 -
Rwork0.271 2130 -
obs--99.03 %

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