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- PDB-3mst: Crystal structure of a Putative nitrate transport protein (TVN010... -

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Basic information

Entry
Database: PDB / ID: 3mst
TitleCrystal structure of a Putative nitrate transport protein (TVN0104) from THERMOPLASMA VOLCANIUM at 1.35 A resolution
ComponentsPutative nitrate transport protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyD-Maltodextrin-Binding Protein; domain 2 - #200 / Protein of unknown function DUF3834 / Protein of unknown function (DUF3834) / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / Unknown ligand / TVG0108190 protein
Function and homology information
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative nitrate transport protein (TVN0104) from THERMOPLASMA VOLCANIUM at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2013Group: Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: 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
Revision 1.6Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative nitrate transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,41512
Polymers27,9311
Non-polymers48511
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.042, 80.040, 42.522
Angle α, β, γ (deg.)90.000, 104.670, 90.000
Int Tables number4
Space group name H-MP1211
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative nitrate transport protein


Mass: 27930.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Gene: TV0103, TVG0108190 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97CJ8

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Non-polymers , 5 types, 284 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. DNA SEQUENCING ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS A SERINE AT POSITION 8 INSTEAD OF AN ALANINE. THE SERINE AT POSITION 8 IS SUPPORTED BY ELECTRON DENSITY.

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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 (%)Description
12.0740.45MAD PHASING WAS ACOMPLISHED WITH 3-WAVELENGTH DATA FROM A SECOND CRYSTAL THAT DIFFRACTED TO 2.2 A. THE INITIAL MODEL BUILT FROM THESE PHASES WAS REFINED AGAINST THE CURRENT 1.35 A DATA.
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Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop4.330.25M calcium chloride, 14.0% 2-propanol, 0.1M sodium acetate pH 4.33, temperature 277K, NANODROP, VAPOR DIFFUSION, SITTING DROP
2772vapor diffusion, sitting drop4.330.25M calcium chloride, 22.0% 2-propanol, 0.1M sodium acetate pH 4.33, temperature 277K, NANODROP, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.91837
SYNCHROTRONSSRL BL11-120.97959, 0.91837, 0.97917
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDMar 10, 2010Flat collimating mirror, toroid focusing mirror
MARMOSAIC 325 mm CCD2CCDFeb 11, 2010Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent monochromator (horizontal focusing)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979591
30.979171
ReflectionResolution: 1.35→41.13 Å / Num. obs: 49540 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.88 % / Biso Wilson estimate: 19.818 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.35-1.40.5032.21622649591,296.5
1.4-1.450.4131620944201,2100
1.45-1.520.2944.11948052811,299.8
1.52-1.60.2115.61828549501,299.8
1.6-1.70.1427.81832249271,299.9
1.7-1.830.10510.41843549341,299.7
1.83-2.020.097162678751151,2100
2.02-2.310.07523.53424549241,299.8
2.31-2.910.05531.13717049861,299.9
2.91-41.130.03742.23659550441,299.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→41.13 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.689 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.048
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3) UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED IN ELECTRON DENSITY FOUND NEAR THE PUTATIVE ACTIVE SITES. (4) CHLORIDE (CL) AND ACETATE (ACT) IONS FROM CRYSTALLIZATION CONDITION, AND ETHYLENE GLYCOL (EDO) MOLECULES FROM CRYO CONDITION ARE MODELED INTO THE STRUCTURE. (5) THE EXPERIMENTAL PHASE RESTRAINTS INCLUDED IN THE REFINEMENT ARE FROM A THREE- WAVELENGTH MAD DATA SET COLLECTED FROM THE SECOND CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.155 2500 5.1 %RANDOM
Rwork0.119 ---
obs0.121 49502 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.72 Å2 / Biso mean: 18.029 Å2 / Biso min: 6.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20.26 Å2
2---0.48 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.35→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 30 273 2112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222089
X-RAY DIFFRACTIONr_bond_other_d0.0040.021435
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9762842
X-RAY DIFFRACTIONr_angle_other_deg0.98433522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16324.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32915380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7121513
X-RAY DIFFRACTIONr_chiral_restr0.1030.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022459
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02430
X-RAY DIFFRACTIONr_mcbond_it2.53131314
X-RAY DIFFRACTIONr_mcbond_other0.923533
X-RAY DIFFRACTIONr_mcangle_it3.53542148
X-RAY DIFFRACTIONr_scbond_it4.8455775
X-RAY DIFFRACTIONr_scangle_it6.8526694
X-RAY DIFFRACTIONr_rigid_bond_restr1.78233524
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 193 -
Rwork0.224 3286 -
all-3479 -
obs--95.58 %

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