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- PDB-3k6w: Apo and ligand bound structures of ModA from the archaeon Methano... -

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Basic information

Entry
Database: PDB / ID: 3k6w
TitleApo and ligand bound structures of ModA from the archaeon Methanosarcina acetivorans
ComponentsSolute-binding protein MA_0280
KeywordsTRANSPORT PROTEIN / ModA / molybdate / Methanosarcina acetivorans / periplasmic binding protein / ABC transporter / ligand / metal-binding protein
Function / homologyTungstate ABC transporter, substrate-binding protein WtpA / tungstate binding / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / MOLYBDATE ION / Uncharacterized solute-binding protein MA_0280
Function and homology information
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsChan, S. / Chernishof, I. / Giuroiu, I. / Sawaya, M.R. / Chiang, J. / Gunsalus, R.P. / Arbing, M.A. / Perry, L.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Apo and ligand-bound structures of ModA from the archaeon Methanosarcina acetivorans
Authors: Chan, S. / Giuroiu, I. / Chernishof, I. / Sawaya, M.R. / Chiang, J. / Gunsalus, R.P. / Arbing, M.A. / Perry, L.J.
History
DepositionOct 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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: Solute-binding protein MA_0280
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6085
Polymers39,1601
Non-polymers4484
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.512, 66.120, 61.460
Angle α, β, γ (deg.)90.000, 95.990, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Solute-binding protein MA_0280


Mass: 39160.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal TEV-cleavable 6xHis-tag / Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0280, MA_0280 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q8TTZ5
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4449.56
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop82.1M ammonium sulfate, 3% (v/v) isopropanol with final concentration of sodium molybdate at 125 mM in the drop, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop82.1M ammonium sulfate, 1% (v/v) isopropanol with final concentration of sodium molybdate at 125 mM in the drop, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211
SYNCHROTRONALS 8.2.221
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 30, 2007
ADSC QUANTUM 3152CCDApr 30, 2007
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→54.07 Å / Num. obs: 13167 / % possible obs: 93.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.071 / Χ2: 1.002 / Net I/σ(I): 13.9
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2 / Num. unique all: 1265 / Rsym value: 0.431 / Χ2: 0.992 / % possible all: 91.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.386 / Cor.coef. Fo:Fc: 0.646
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→54.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.832 / SU B: 17.964 / SU ML: 0.202 / SU R Cruickshank DPI: 0.516 / SU Rfree: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.516 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 681 5.2 %RANDOM
Rwork0.207 ---
obs0.208 13107 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 118.09 Å2 / Biso mean: 37.046 Å2 / Biso min: 9.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å2-3.43 Å2
2--2.06 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.45→54.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 20 28 2464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222482
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.9773389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8515311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30525.763118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05415392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.143159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211913
X-RAY DIFFRACTIONr_mcbond_it1.80321559
X-RAY DIFFRACTIONr_mcangle_it2.91832518
X-RAY DIFFRACTIONr_scbond_it2.1282923
X-RAY DIFFRACTIONr_scangle_it3.0363871
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 55 -
Rwork0.292 895 -
all-950 -
obs--91.61 %
Refinement TLS params.Method: refined / Origin x: 18.3706 Å / Origin y: 21.4695 Å / Origin z: -7.0296 Å
111213212223313233
T0.0819 Å20.0183 Å20.0052 Å2-0.1376 Å20.0711 Å2--0.1003 Å2
L3.3758 °20.5744 °22.1298 °2-1.5098 °20.4859 °2--2.09 °2
S-0.0084 Å °0.4877 Å °0.1227 Å °0.1858 Å °-0.0493 Å °-0.1934 Å °0.1273 Å °0.2447 Å °0.0577 Å °

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