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- PDB-3k6v: M. acetivorans Molybdate-Binding Protein (ModA) in Citrate-Bound ... -

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Open data


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Basic information

Entry
Database: PDB / ID: 3k6v
TitleM. acetivorans Molybdate-Binding Protein (ModA) in Citrate-Bound Open Form
ComponentsSolute-binding protein MA_0280
KeywordsTRANSPORT PROTEIN / ModA / molybdate / Methanosarcina acetivorans / periplasmic binding protein / ABC transporter / ligand / metal-binding protein
Function / homology
Function and homology information


tungstate binding / molybdate ion binding / molybdate ion transport
Similarity search - Function
Tungstate ABC transporter, substrate-binding protein WtpA / : / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Uncharacterized solute-binding protein MA_0280
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsChan, S. / Giuroiu, I. / Chernishof, 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: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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)39,3522
Polymers39,1601
Non-polymers1921
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.629, 81.629, 104.636
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 4mM Sodium Sulfate, 1.4M Ammonium Citrate, pH6.0, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.69→58.62 Å / Num. obs: 84835 / % possible obs: 96.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.054 / Rsym value: 0.04 / Χ2: 0.995 / Net I/σ(I): 16.3
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.26 / Num. unique all: 7182 / Rsym value: 0.472 / Χ2: 1.004 / % possible all: 82.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.29 / Cor.coef. Fo:Fc: 0.76
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: 1.69→58.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.865 / SU B: 4.278 / SU ML: 0.065 / SU R Cruickshank DPI: 0.097 / SU Rfree: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2184 5 %RANDOM
Rwork0.189 ---
obs0.19 43968 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.29 Å2 / Biso mean: 19.883 Å2 / Biso min: 11.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.47 Å20 Å2
2--0.93 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.69→58.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 13 294 2730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222501
X-RAY DIFFRACTIONr_angle_refined_deg0.9751.973416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3645315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45226.032126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15315398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.793159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211957
X-RAY DIFFRACTIONr_mcbond_it0.3461.51566
X-RAY DIFFRACTIONr_mcangle_it0.67622536
X-RAY DIFFRACTIONr_scbond_it0.9973935
X-RAY DIFFRACTIONr_scangle_it1.7374.5878
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 159 -
Rwork0.275 3007 -
all-3166 -
obs--97.48 %
Refinement TLS params.Method: refined / Origin x: 26.3992 Å / Origin y: 44.2635 Å / Origin z: 14.6913 Å
111213212223313233
T0.008 Å20.0015 Å2-0.0014 Å2-0.0251 Å20.0004 Å2--0.0276 Å2
L1.0005 °2-0.4701 °20.8833 °2-0.6358 °2-0.7898 °2--2.046 °2
S-0.017 Å °0.035 Å °0.0112 Å °-0.0028 Å °-0.0146 Å °0.0274 Å °-0.0387 Å °0.1454 Å °0.0316 Å °

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