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- PDB-3c4j: ABC protein ArtP in complex with ATP-gamma-S -

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Basic information

Entry
Database: PDB / ID: 3c4j
TitleABC protein ArtP in complex with ATP-gamma-S
ComponentsAmino acid ABC transporter (ArtP)
KeywordsHYDROLASE / ABC Domain / ATPase
Function / homology
Function and homology information


polar-amino-acid-transporting ATPase / ABC-type amino acid transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
ABC-type amino acid transport system, ATPase component, HisP-type / : / 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 ...ABC-type amino acid transport system, ATPase component, HisP-type / : / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Amino acid ABC transporter
Similarity search - Component
Biological speciesGeobacillus Stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsThaben, P.F. / Eckey, V. / Scheffel, F. / Saenger, W. / Schneider, E. / Vahedi-Faridi, A.
CitationJournal: To be Published
Title: Crystal Structures of the ATP-binding cassette (ABC) Protein ArtP from Geobacillus stearothermophilus in complexes with nucleotides and nucleotide analogs reveal an intermediate semiclosed ...Title: Crystal Structures of the ATP-binding cassette (ABC) Protein ArtP from Geobacillus stearothermophilus in complexes with nucleotides and nucleotide analogs reveal an intermediate semiclosed dimer in the post hydrolyses state and an asymmetry in the dimerisation region
Authors: Thaben, P.F. / Eckey, V. / Scheffel, F. / Allings, C. / Behlke, J. / Saenger, W. / Schneider, E. / Vahedi-Faridi, A.
History
DepositionJan 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 15, 2012Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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 / 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_asym_id / _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.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Amino acid ABC transporter (ArtP)
B: Amino acid ABC transporter (ArtP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9056
Polymers58,8102
Non-polymers1,0954
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-38 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.155, 83.437, 69.569
Angle α, β, γ (deg.)90.000, 107.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amino acid ABC transporter (ArtP)


Mass: 29405.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus Stearothermophilus (bacteria)
Strain: DSMZ 13240 / Gene: artp / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(de3)plyss
References: UniProt: D0VWX4*PLUS, polar-amino-acid-transporting ATPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 1.4M Na-Acetate, 0.1M Hepes, 0.01M MgCl2, pH7.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 20071 / % possible obs: 87.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.101 / Χ2: 0.909 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.432.80.34914160.839161.8
2.43-2.5330.34315130.862167.7
2.53-2.653.20.27217330.841175.9
2.65-2.793.30.25519550.803185.3
2.79-2.963.50.21620740.834191.9
2.96-3.193.70.17722030.872196
3.19-3.5140.12322600.847198.6
3.51-4.024.20.09522770.965199.9
4.02-5.064.20.08223011.0131100
5.06-504.20.0723391.032199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.72 Å
Translation2.5 Å41.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OLJ

2olj


Resolution: 2.33→41.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.337 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.678 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1045 5.2 %RANDOM
Rwork0.221 ---
obs0.224 20049 87.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0.35 Å2
2---0.09 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.33→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 64 228 4084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223920
X-RAY DIFFRACTIONr_angle_refined_deg1.1612.0025286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5485482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51524.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44915742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9621524
X-RAY DIFFRACTIONr_chiral_restr0.0820.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022866
X-RAY DIFFRACTIONr_nbd_refined0.1860.21970
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22645
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2277
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.26
X-RAY DIFFRACTIONr_mcbond_it0.4411.52474
X-RAY DIFFRACTIONr_mcangle_it0.77723872
X-RAY DIFFRACTIONr_scbond_it0.9231599
X-RAY DIFFRACTIONr_scangle_it1.5514.51414
LS refinement shellResolution: 2.332→2.393 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 49 -
Rwork0.261 919 -
all-968 -
obs--57.14 %

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