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- PDB-1vpl: Crystal structure of ABC transporter ATP-binding protein (TM0544)... -

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Basic information

Entry
Database: PDB / ID: 1vpl
TitleCrystal structure of ABC transporter ATP-binding protein (TM0544) from Thermotoga maritima at 2.10 A resolution
ComponentsABC transporter, ATP-binding proteinATP-binding cassette transporter
KeywordsLYASE / TM0544 / ABC TRANSPORTER ATP-BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


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
ABC transporter, ATP-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of ABC transporter ATP-binding protein (TM0544) from Thermotoga maritima at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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_special_symmetry / 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_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: ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8193
Polymers28,6271
Non-polymers1922
Water2,450136
1
A: ABC transporter, ATP-binding protein
hetero molecules

A: ABC transporter, ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6386
Polymers57,2542
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)90.590, 90.590, 72.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

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Components

#1: Protein ABC transporter, ATP-binding protein / ATP-binding cassette transporter


Mass: 28627.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0544 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ14
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.98 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4
Details: 0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 2.1→39.23 Å / Num. obs: 20216 / % possible obs: 99.2 % / Redundancy: 8 % / Biso Wilson estimate: 36.34 Å2 / Rsym value: 0.119 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 1371 / Rsym value: 0.66 / % possible all: 92.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.2.0001refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JI0

1ji0


Resolution: 2.1→39.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.791 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21581 1030 5.1 %RANDOM
Rwork0.17139 ---
obs0.17372 19181 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.602 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.89 Å20 Å2
2--1.79 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 10 136 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221932
X-RAY DIFFRACTIONr_bond_other_d0.0010.021875
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9822602
X-RAY DIFFRACTIONr_angle_other_deg0.87534356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33823.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40615384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6351518
X-RAY DIFFRACTIONr_chiral_restr0.10.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.2120.2385
X-RAY DIFFRACTIONr_nbd_other0.1830.21987
X-RAY DIFFRACTIONr_nbtor_other0.0910.21196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3050.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.212
X-RAY DIFFRACTIONr_mcbond_it2.69831302
X-RAY DIFFRACTIONr_mcbond_other0.5723494
X-RAY DIFFRACTIONr_mcangle_it3.44551933
X-RAY DIFFRACTIONr_scbond_it6.9638791
X-RAY DIFFRACTIONr_scangle_it9.4911669
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 69 5.05 %
Rwork0.231 1297 -
Refinement TLS params.Method: refined / Origin x: 28.0603 Å / Origin y: 34.1259 Å / Origin z: 15.2603 Å
111213212223313233
T-0.2159 Å20.0511 Å2-0.0093 Å2--0.0782 Å20.0042 Å2---0.0785 Å2
L0.6622 °2-0.2421 °2-0.6643 °2-0.631 °20.164 °2--4.7684 °2
S0.0373 Å °0.0372 Å °0.0381 Å °-0.025 Å °0.0264 Å °0.0124 Å °0.0859 Å °0.1137 Å °-0.0638 Å °
Refinement TLS groupSelection: ALL

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