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- PDB-1g9x: CHARACTERIZATION OF THE TWINNING STRUCTURE OF MJ1267, AN ATP-BIND... -

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Entry
Database: PDB / ID: 1g9x
TitleCHARACTERIZATION OF THE TWINNING STRUCTURE OF MJ1267, AN ATP-BINDING CASSETTE OF AN ABC TRANSPORTER
ComponentsHIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
KeywordsSTRUCTURAL GENOMICS / Hemihedral twinning structure / ATP-binding cassette / ABC transporter
Function / homology
Function and homology information


amino acid transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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 ...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 / METHYL MERCURY ION / Probable branched-chain amino acid transport ATP-binding protein LivG
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYuan, Y.-R. / Hunt, J.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural characterization of an MJ1267 ATP-binding cassette crystal with a complex pattern of twinning caused by promiscuous fiber packing.
Authors: Yuan, Y.R. / Martsinkevich, O. / Hunt, J.F.
History
DepositionNov 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
B: HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
C: HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,05812
Polymers87,0563
Non-polymers2,0019
Water2,576143
1
A: HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6864
Polymers29,0191
Non-polymers6673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6864
Polymers29,0191
Non-polymers6673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6864
Polymers29,0191
Non-polymers6673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.310, 117.310, 42.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT ATP-BINDING PROTEIN


Mass: 29018.715 Da / Num. of mol.: 3 / Fragment: MJ1267 / Mutation: N31C, N1031C, N2031C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: STRUCTURAL DNA / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q58663
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MMC / METHYL MERCURY ION / Methylmercury


Mass: 215.625 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH3Hg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris/HCl, PEG 2000MME, Glycerol, Mg-ADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 310 K / pH: 8.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
136 mg/mlprotein1drop
210 mMTris-HCl1droppH8.8
320 mMMg-ADP1drop
416 %(w/v)PEG33501drop
530 %(v/v)ethylene glycol1drop
620 %(v/v)glycerol1drop
74 mM1dropMgCl2
80.2 mMdithiothreitol1drop
9200 mMMES1droppH5.9
1015-20 %(w/v)PEG33501reservoir
1115 %(v/v)ethylene glycol1reservoir
1210 %(v/v)glycerol1reservoir
130.1 mMdithiothreitol1reservoir
14100 mMMES1reservoirpH5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→14.66 Å / Num. all: 18818 / Num. obs: 18662 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.58 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.4
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.068 / % possible all: 92
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / % possible obs: 92.6 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 90.7 % / Redundancy: 1.43 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 7.08

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: coordination of C2 MJ1267

Resolution: 2.6→14.66 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1077889.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1730 9.3 %RANDOM
Rwork0.153 ---
obs0.153 18662 93.8 %-
all-18818 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.26 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.6→14.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6006 0 90 143 6239
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it1.432
X-RAY DIFFRACTIONc_scangle_it2.132.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 278 9.1 %
Rwork0.187 2788 -
obs--92 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22
LS refinement shell
*PLUS
Rfactor Rfree: 0.357 / Rfactor Rwork: 0.351

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