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- PDB-3tif: Dimeric structure of a post-hydrolysis state of the ATP-binding c... -

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Basic information

Entry
Database: PDB / ID: 3tif
TitleDimeric structure of a post-hydrolysis state of the ATP-binding cassette MJ0796 bound to ADP and Pi
ComponentsUncharacterized ABC transporter ATP-binding protein MJ0796
KeywordsRNA BINDING PROTEIN / Nucleotide-binding domain / ABC transporter ATPase / ATP binding
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ISOPROPYL ALCOHOL / HYDROGENPHOSPHATE ION / Uncharacterized ABC transporter ATP-binding protein MJ0796
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7995 Å
AuthorsSutton, R.B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Kinetics of the association/dissociation cycle of an ATP-binding cassette nucleotide-binding domain.
Authors: Zoghbi, M.E. / Fuson, K.L. / Sutton, R.B. / Altenberg, G.A.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Sep 13, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.pdbx_ptnr1_label_alt_id / _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_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 MJ0796
B: Uncharacterized ABC transporter ATP-binding protein MJ0796
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,70811
Polymers53,4362
Non-polymers1,2739
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-52 kcal/mol
Surface area20170 Å2
MethodPISA
2
A: Uncharacterized ABC transporter ATP-binding protein MJ0796
B: Uncharacterized ABC transporter ATP-binding protein MJ0796
hetero molecules

A: Uncharacterized ABC transporter ATP-binding protein MJ0796
B: Uncharacterized ABC transporter ATP-binding protein MJ0796
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,41722
Polymers106,8714
Non-polymers2,54518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area14040 Å2
ΔGint-114 kcal/mol
Surface area36880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.649, 106.347, 117.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized ABC transporter ATP-binding protein MJ0796


Mass: 26717.824 Da / Num. of mol.: 2 / Mutation: I2V, E171Q and G174W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0796 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q58206

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Non-polymers , 5 types, 220 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PI / HYDROGENPHOSPHATE ION / Phosphate


Mass: 95.979 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO4P
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG4000, 10% isopropanol, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSSRL BL7-110.9796
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 10, 2011
Rigaku ScreenMachine2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
21.54181
ReflectionResolution: 1.799→33.4 Å / Num. all: 46824 / Num. obs: 46824 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 37.02 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 36
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueDiffraction-ID% possible all
1.799-1.915.377450.581,2100
1.91-2.065.477180.271,299.9
2.06-2.275.477660.1421,2100
2.27-2.65.378210.0821,299.9
2.6-3.275.378250.041,299.8
3.27-505.277370.0241,295.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L2T

1l2t


Resolution: 1.7995→33.389 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 3651 7.8 %random
Rwork0.2029 ---
obs0.2054 46819 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.31 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.777 Å20 Å2-0 Å2
2--0.3567 Å2-0 Å2
3----5.1337 Å2
Refinement stepCycle: LAST / Resolution: 1.7995→33.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 78 211 3962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063814
X-RAY DIFFRACTIONf_angle_d1.1145137
X-RAY DIFFRACTIONf_dihedral_angle_d12.2971483
X-RAY DIFFRACTIONf_chiral_restr0.112579
X-RAY DIFFRACTIONf_plane_restr0.003657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7995-1.82310.30661340.27571548X-RAY DIFFRACTION95
1.8231-1.84810.31841820.27331597X-RAY DIFFRACTION100
1.8481-1.87450.34521340.26481637X-RAY DIFFRACTION100
1.8745-1.90250.2781370.27781668X-RAY DIFFRACTION100
1.9025-1.93220.3361330.2711633X-RAY DIFFRACTION100
1.9322-1.96390.34041530.25941659X-RAY DIFFRACTION100
1.9639-1.99770.26771340.25181625X-RAY DIFFRACTION100
1.9977-2.03410.28251310.23951672X-RAY DIFFRACTION100
2.0341-2.07320.31430.24491634X-RAY DIFFRACTION100
2.0732-2.11550.3051510.23961638X-RAY DIFFRACTION100
2.1155-2.16150.28281460.22841650X-RAY DIFFRACTION100
2.1615-2.21180.26581320.2181665X-RAY DIFFRACTION100
2.2118-2.26710.28211350.22531661X-RAY DIFFRACTION100
2.2671-2.32830.24611370.22061658X-RAY DIFFRACTION100
2.3283-2.39680.3091380.21861668X-RAY DIFFRACTION100
2.3968-2.47420.26681360.22551661X-RAY DIFFRACTION100
2.4742-2.56260.30711360.23641659X-RAY DIFFRACTION100
2.5626-2.66510.30021390.24621668X-RAY DIFFRACTION100
2.6651-2.78640.25961370.23991671X-RAY DIFFRACTION100
2.7864-2.93320.24411360.22531662X-RAY DIFFRACTION99
2.9332-3.11680.28911380.22141666X-RAY DIFFRACTION100
3.1168-3.35730.22741400.21221687X-RAY DIFFRACTION100
3.3573-3.69480.2421380.19281686X-RAY DIFFRACTION100
3.6948-4.22850.20711410.1671693X-RAY DIFFRACTION100
4.2285-5.3240.18441420.16111719X-RAY DIFFRACTION100
5.324-33.39420.17451480.18451783X-RAY DIFFRACTION99

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