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- PDB-3k6x: M. acetivorans Molybdate-Binding Protein (ModA) in Molybdate-Boun... -

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Basic information

Entry
Database: PDB / ID: 3k6x
TitleM. acetivorans Molybdate-Binding Protein (ModA) in Molybdate-Bound Close Form with 2 Molecules in Asymmetric Unit Forming Beta Barrel
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 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
MOLYBDATE ION / Uncharacterized solute-binding protein MA_0280
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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 / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Solute-binding protein MA_0280
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,40912
Polymers78,3202
Non-polymers1,08810
Water1,71195
1
A: Solute-binding protein MA_0280
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7046
Polymers39,1601
Non-polymers5445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Solute-binding protein MA_0280
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7046
Polymers39,1601
Non-polymers5445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.195, 65.587, 94.768
Angle α, β, γ (deg.)90.000, 123.950, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLUGLU1BB44 - 5746 - 59
21THRTHRGLUGLU1AA44 - 5746 - 59
12LEULEUHISHIS4BB58 - 6660 - 68
22LEULEUHISHIS4AA58 - 6660 - 68
13GLYGLYARGARG6BB68 - 7370 - 75
23GLYGLYARGARG6AA68 - 7370 - 75
14GLUGLUSERSER5BB74 - 8176 - 83
24GLUGLUSERSER5AA74 - 8176 - 83
15ARGARGALAALA1BB83 - 11685 - 118
25ARGARGALAALA1AA83 - 11685 - 118
16PHEPHEASNASN2BB118 - 129120 - 131
26PHEPHEASNASN2AA118 - 129120 - 131
17GLUGLULEULEU5BB130 - 146132 - 148
27GLUGLULEULEU5AA130 - 146132 - 148
18ARGARGPROPRO1BB147 - 209149 - 211
28ARGARGPROPRO1AA147 - 209149 - 211
19ALAALAARGARG4BB210 - 224212 - 226
29ALAALAARGARG4AA210 - 224212 - 226
110SERSERLEULEU5BB225 - 242227 - 244
210SERSERLEULEU5AA225 - 242227 - 244
111TYRTYRGLNGLN2BB243 - 251245 - 253
211TYRTYRGLNGLN2AA243 - 251245 - 253
112HISHISPROPRO5BB252 - 261254 - 263
212HISHISPROPRO5AA252 - 261254 - 263
113ALAALAVALVAL2BB262 - 287264 - 289
213ALAALAVALVAL2AA262 - 287264 - 289
114THRTHRASNASN1BB288 - 304290 - 306
214THRTHRASNASN1AA288 - 304290 - 306
115SERSERALAALA3BB305 - 308307 - 310
215SERSERALAALA3AA305 - 308307 - 310
116THRTHRILEILE2BB309 - 325311 - 327
216THRTHRILEILE2AA309 - 325311 - 327
117GLUGLUVALVAL4BB326 - 333328 - 335
217GLUGLUVALVAL4AA326 - 333328 - 335
118PROPROGLYGLY1BB334 - 339336 - 341
218PROPROGLYGLY1AA334 - 339336 - 341
119LYSLYSGLUGLU2BB340 - 345342 - 347
219LYSLYSGLUGLU2AA340 - 345342 - 347
120GLUGLUHOHHOH5BB - N346 - 354348
220GLUGLUHOHHOH5AA - M346 - 354348

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Components

#1: Protein Solute-binding protein MA_0280


Mass: 39160.156 Da / Num. of mol.: 2
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


Mass: 159.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: MoO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.4M ammonium sulfate, 4% (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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→57.74 Å / Num. obs: 31325 / % possible obs: 87.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.062 / Rsym value: 0.045 / Χ2: 0.993 / Net I/σ(I): 9.7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.13 / Num. unique all: 2973 / Rsym value: 0.279 / Χ2: 1.003 / % possible all: 84.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.701 / Cor.coef. Fo:Fc: 0.289
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: 2.25→57.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.244 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.724 / SU B: 15.899 / SU ML: 0.207 / SU R Cruickshank DPI: 0.424 / SU Rfree: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1592 5.1 %RANDOM
Rwork0.237 ---
obs0.238 31302 87.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 116.82 Å2 / Biso mean: 36.391 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å22 Å2
2--1.59 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.25→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4992 0 50 95 5137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225136
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9777017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9055640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.58825.755245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.87115800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9471518
X-RAY DIFFRACTIONr_chiral_restr0.1010.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213956
X-RAY DIFFRACTIONr_mcbond_it1.04923218
X-RAY DIFFRACTIONr_mcangle_it1.71535199
X-RAY DIFFRACTIONr_scbond_it1.1321918
X-RAY DIFFRACTIONr_scangle_it1.66831818
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1325TIGHT POSITIONAL0.10.05
763MEDIUM POSITIONAL0.170.5
277LOOSE POSITIONAL0.225
1325TIGHT THERMAL1.190.5
763MEDIUM THERMAL1.332
277LOOSE THERMAL1.5210
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 106 -
Rwork0.337 2009 -
all-2115 -
obs--80.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1494-0.01-1.26952.4166-0.41532.05880.16060.60920.1444-0.2921-0.0939-0.1917-0.0704-0.3711-0.06660.05280.04740.02790.11970.03360.023328.058821.25420.2684
24.1292-0.6903-1.26392.62770.29251.83240.0141-0.4299-0.01710.26180.04870.1687-0.10740.2024-0.06280.0456-0.01780.01860.05620.00080.016618.981722.054338.82
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 352
2X-RAY DIFFRACTION2B43 - 352

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