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- PDB-3gwi: Crystal Structure of Mg-ATPase Nucleotide binding domain -

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Basic information

Entry
Database: PDB / ID: 3gwi
TitleCrystal Structure of Mg-ATPase Nucleotide binding domain
ComponentsMagnesium-transporting ATPase, P-type 1
KeywordsHYDROLASE / P-type ATPase / nucleotide binding / ATP binding / MgtA / membrane protein / Cell inner membrane / Cell membrane / Magnesium / Metal-binding / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


P-type Mg2+ transporter / P-type magnesium transporter activity / magnesium ion transmembrane transport / P-type ion transporter activity / ATPase-coupled monoatomic cation transmembrane transporter activity / cellular response to magnesium ion / membrane => GO:0016020 / intracellular membrane-bounded organelle / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIIB / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N ...P-type ATPase, subfamily IIIB / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Magnesium-transporting ATPase, P-type 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHakansson, K.O.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The structure of Mg-ATPase nucleotide-binding domain at 1.6 A resolution reveals a unique ATP-binding motif
Authors: Hakansson, K.O.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and data collection of the nucleotide-binding domain of Mg-ATPase
Authors: Hakansson, K.O. / Curovic, A.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7463
Polymers19,5541
Non-polymers1922
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.620, 99.620, 46.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-14-

HOH

21A-23-

HOH

31A-109-

HOH

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Components

#1: Protein Magnesium-transporting ATPase, P-type 1 / Mg-ATPase / Mg(2+) transport ATPase / P-type 1


Mass: 19554.082 Da / Num. of mol.: 1 / Fragment: N-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: mgtA / Plasmid: pQE-40 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: P0ABB8, EC: 3.6.3.2
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 2% PEG 400, 2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.53→27.63 Å / Num. all: 35560 / Num. obs: 33678 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.1
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 6 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 10.1 / Num. unique all: 5643 / % possible all: 70

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.388 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21981 1556 5 %RANDOM
Rwork0.1907 ---
obs0.19214 29519 100 %-
all-31298 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 10 272 1595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211341
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9631815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4423.97168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46915245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7281513
X-RAY DIFFRACTIONr_chiral_restr0.0790.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021002
X-RAY DIFFRACTIONr_nbd_refined0.1980.2626
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2936
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.229
X-RAY DIFFRACTIONr_mcbond_it0.881.5839
X-RAY DIFFRACTIONr_mcangle_it1.43221318
X-RAY DIFFRACTIONr_scbond_it2.2833555
X-RAY DIFFRACTIONr_scangle_it3.7834.5497
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 98 -
Rwork0.2 2137 -
obs--100 %

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