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- PDB-1f3o: Crystal structure of MJ0796 ATP-binding cassette -

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Basic information

Entry
Database: PDB / ID: 1f3o
TitleCrystal structure of MJ0796 ATP-binding cassette
ComponentsHYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0796
KeywordsSTRUCTURAL GENOMICS / Transporter
Function / homology
Function and homology information


transmembrane transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD / 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 ...MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD / 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
ADENOSINE-5'-DIPHOSPHATE / Uncharacterized ABC transporter ATP-binding protein MJ0796
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsYuan, Y.-R. / Hunt, J.F.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The crystal structure of the MJ0796 ATP-binding cassette. Implications for the structural consequences of ATP hydrolysis in the active site of an ABC transporter.
Authors: Yuan, Y.R. / Blecker, S. / Martsinkevich, O. / Millen, L. / Thomas, P.J. / Hunt, J.F.
History
DepositionJun 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _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

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Assembly

Deposited unit
A: HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0796
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3833
Polymers26,9321
Non-polymers4522
Water1,15364
1
A: HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0796
hetero molecules

A: HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0796
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7676
Polymers53,8642
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)55.210, 65.200, 126.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a dimer

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Components

#1: Protein HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN MJ0796


Mass: 26931.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: PET28A / Gene (production host): GENOMIC DNA / Production host: Escherichia coli (E. coli) / References: UniProt: Q58206
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 4000, Ammonium Acetate, Glycerol, ADP, Magnesium Chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris1drop
210 mMMgADP1drop
32 mg/mlprotein1drop
412 %PEG40001reservoir
530 %(v/v)glycerol1reservoir
6200 mM1reservoirMgCl2
7100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.932
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 25396 / Num. obs: 24520 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 4.42 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 5.5
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 3.9 % / % possible all: 74.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
RefinementResolution: 2.7→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: X-Plor 3.851
RfactorNum. reflection% reflectionSelection details
Rfree0.277 663 11.1 %RANDOM
Rwork0.204 ---
obs-5971 90.9 %-
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.97 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 28 64 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_improper_angle_d1.67
X-RAY DIFFRACTIONx_mcbond_it6.531.5
X-RAY DIFFRACTIONx_mcangle_it9.652
X-RAY DIFFRACTIONx_scbond_it9.672
X-RAY DIFFRACTIONx_scangle_it12.752.5
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.456 64 10.7 %
Rwork0.368 535 -
obs--74.5 %
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 11.1 % / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.67
X-RAY DIFFRACTIONx_mcbond_it6.531.5
X-RAY DIFFRACTIONx_scbond_it9.672
X-RAY DIFFRACTIONx_mcangle_it9.652
X-RAY DIFFRACTIONx_scangle_it12.752.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.456 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.368

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