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- PDB-1g29: MALK -

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Basic information

Entry
Database: PDB / ID: 1g29
TitleMALK
ComponentsMALTOSE TRANSPORT PROTEIN MALK
KeywordsSUGAR BINDING PROTEIN / ATPase / active transport / maltose uptake and regulation
Function / homology
Function and homology information


ABC-type maltose transporter / ABC-type maltose transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...MalK, OB fold domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / AMMONIUM ION / PYROPHOSPHATE 2- / Trehalose/maltose import ATP-binding protein MalK
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsDiederichs, K. / Diez, J. / Greller, G. / Mueller, C. / Breed, J. / Schnell, C. / Vonrhein, C. / Boos, W. / Welte, W.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis.
Authors: Diederichs, K. / Diez, J. / Greller, G. / Muller, C. / Breed, J. / Schnell, C. / Vonrhein, C. / Boos, W. / Welte, W.
History
DepositionOct 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
1: MALTOSE TRANSPORT PROTEIN MALK
2: MALTOSE TRANSPORT PROTEIN MALK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,65359
Polymers83,7172
Non-polymers1,93657
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-377 kcal/mol
Surface area34030 Å2
MethodPISA
2
1: MALTOSE TRANSPORT PROTEIN MALK
hetero molecules

1: MALTOSE TRANSPORT PROTEIN MALK
hetero molecules

2: MALTOSE TRANSPORT PROTEIN MALK
hetero molecules

2: MALTOSE TRANSPORT PROTEIN MALK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,306118
Polymers167,4344
Non-polymers3,872114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_646-x+3/2,y-1/2,-z+11
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area21200 Å2
ΔGint-895 kcal/mol
Surface area66700 Å2
MethodPISA
3
1: MALTOSE TRANSPORT PROTEIN MALK
hetero molecules

2: MALTOSE TRANSPORT PROTEIN MALK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,65359
Polymers83,7172
Non-polymers1,93657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_646-x+3/2,y-1/2,-z+11
Buried area9630 Å2
ΔGint-434 kcal/mol
Surface area34320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.718, 65.705, 77.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules 12

#1: Protein MALTOSE TRANSPORT PROTEIN MALK / MALK


Mass: 41858.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis (archaea) / Gene: MALK / Plasmid: PGG200 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9YGA6

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Non-polymers , 7 types, 453 molecules

#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#7: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2M ammonium sulfate, 5% dioxane, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMprotein1drop
21 mMADP1drop
42 Mammonium sulfate1reservoir
55 %dioxane1reservoir
6100 mMTris-HCl1reservoir
3reservoir1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8424 Å / Relative weight: 1
ReflectionResolution: 1.86→34.26 Å / Num. all: 82679 / Num. obs: 82679 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 20.6 Å2 / Limit h max: 102 / Limit h min: 0 / Limit k max: 35 / Limit k min: 0 / Limit l max: 41 / Limit l min: 0 / Observed criterion F max: 4524403.2 / Observed criterion F min: 12.92 / Rmerge(I) obs: 0.036 / Net I/σ(I): 24.6
Reflection shellResolution: 1.86→1.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2430 / Rsym value: 0.235 / % possible all: 93.8
Reflection shell
*PLUS
% possible obs: 93.8 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→34.26 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.67 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1552 2 %random
Rwork0.211 ---
all-78040 --
obs-77441 99.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 41.6539 Å2 / ksol: 0.382079 e/Å3
Displacement parametersBiso max: 82.58 Å2 / Biso mean: 31.76 Å2 / Biso min: 7.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--6.89 Å20 Å2
3----5.53 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 88 396 6362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_torsion_deg24.3
X-RAY DIFFRACTIONx_torsion_impr_deg1.07
X-RAY DIFFRACTIONx_mcbond_it1.471.5
X-RAY DIFFRACTIONx_mcangle_it2.272
X-RAY DIFFRACTIONx_scbond_it2.462
X-RAY DIFFRACTIONx_scangle_it3.712.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 2 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.2551930.25493450.0189655953898.8
1.99-2.090.2061930.20692970.0159608949098.8
2.09-2.220.2031910.20494310.0159701962299.2
2.22-2.390.2251920.22593890.0169664958199.1
2.39-2.630.1921900.19194690.0149734965999.2
2.63-3.020.2021950.20194920.0149752968799.3
3.02-3.80.2061950.20795410.0159817973699.2
3.8-34.260.2172030.21699250.015101901012899.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2pop.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3water_rep.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4ion.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5dox.param&_1_TOPOLOGY_INFILE_5
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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