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- PDB-39nc: The crystal structure of a solute-binding protein (L70S and N280D... -

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Basic information

Entry
Database: PDB / ID: 39nc
TitleThe crystal structure of a solute-binding protein (L70S and N280D mutant) from Trichormus variabilis ATCC 29413 in complex with Lysine
ComponentsAmino acid/amide ABC transporter substrate-binding protein, HAAT family
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / Midwest Center for Structural Genomics / MCSG
Function / homology: / Leucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / LYSINE / Amino acid/amide ABC transporter substrate-binding protein, HAAT family
Function and homology information
Biological speciesTrichormus variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsTan, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094585 United States
CitationJournal: To Be Published
Title: The crystal structure of a solute-binding protein (L70S and N280D mutant) from Trichormus variabilis ATCC 29413 in complex with Lysine
Authors: Tan, K. / Joachimiak, A.
History
DepositionOct 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5454
Polymers42,3381
Non-polymers2073
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.005, 114.005, 55.766
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Amino acid/amide ABC transporter substrate-binding protein, HAAT family


Mass: 42338.285 Da / Num. of mol.: 1 / Mutation: L70S, N280D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichormus variabilis ATCC 29413 (bacteria)
Gene: Ava_0465 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: Q3MFZ5
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.17 M Ammonium Acetate, 0.085 M Sodium Acetate:HCl, 25.5% (w/v) PEG 4000 and 15% (v/v) Glycerol and 10 mM Lysine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.68→40 Å / Num. obs: 47198 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 26.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.019 / Net I/σ(I): 64.5
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2312 / CC1/2: 0.886 / Rpim(I) all: 0.224 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX2.1_6048refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→39.86 Å / SU ML: 0.2142 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2119 2318 4.92 %
Rwork0.1957 44803 -
obs0.1965 47121 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.36 Å2
Refinement stepCycle: LAST / Resolution: 1.68→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 12 197 2916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01192792
X-RAY DIFFRACTIONf_angle_d1.12473804
X-RAY DIFFRACTIONf_chiral_restr0.0703448
X-RAY DIFFRACTIONf_plane_restr0.0083505
X-RAY DIFFRACTIONf_dihedral_angle_d17.52061017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.33261490.30132604X-RAY DIFFRACTION99.49
1.71-1.750.31991320.28242625X-RAY DIFFRACTION99.86
1.75-1.790.34681220.26252625X-RAY DIFFRACTION99.89
1.79-1.840.29961480.24612608X-RAY DIFFRACTION99.86
1.84-1.890.27491290.25122591X-RAY DIFFRACTION99.78
1.89-1.940.28971290.24972647X-RAY DIFFRACTION99.96
1.94-2.010.28491530.25352618X-RAY DIFFRACTION99.93
2.01-2.080.29231440.23682633X-RAY DIFFRACTION100
2.08-2.160.26191340.21752620X-RAY DIFFRACTION99.96
2.16-2.260.21131380.22312620X-RAY DIFFRACTION100
2.26-2.380.21741500.21972628X-RAY DIFFRACTION99.82
2.38-2.530.25151350.2172636X-RAY DIFFRACTION99.89
2.53-2.720.21121340.20642629X-RAY DIFFRACTION99.89
2.72-30.22541100.20962668X-RAY DIFFRACTION99.75
3-3.430.19641560.19252651X-RAY DIFFRACTION99.79
3.43-4.320.17441220.16142672X-RAY DIFFRACTION99.93
4.32-39.860.14591330.14452728X-RAY DIFFRACTION99.65
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)
10.67077172138491-0.394580516513460.0899372365051420.82156054907853-0.194688195998091.16150898301250.0636730689063660.137864263198930.1158846-0.435355463318210.198536497067890.66439050.2803008145406-0.13769553638131-0.18013190.33280006262535-0.065461705041562-0.210920751875390.279103867168890.116042389662890.39078164174109-29.702-23.678-10.112
22.1708815752890.0455917643413450.081930858728413.275932189427-1.67973444150343.55341793676490.015212182053101-0.113440372262060.124720.399146890053080.100222615809630.38625996-0.19654393247051-0.061886382928124-0.1330.3412256266587-0.0328594896971050.0349546416799410.204035734161920.0069486272429040.20018366972848-31.372-41.23114.963
30.2593329248348-0.238805597202510.373673331789960.23387331122641-0.195758653990751.1349467787356-0.140260248386550.53357608259920.144904-0.478111938882440.477508351709961.1985990890.2324504913045-0.5787796569966-0.6500820.33049266700935-0.28884991232409-0.323379449263290.713947350652840.498961092850521.1717539608331-46.865-34.536-2.905
40.725625369278390.51430818023175-0.480132015347480.50892351750803-0.375969394764061.30302369106430.218642814842730.0351603522364-0.072230.0731266812383160.564378412199611.06390009-0.25841701351965-0.54779893861462-0.431840.25142120736564-0.0030805586550507-0.0922014222101570.406772146420270.287371895743910.71863140718055-38.657-14.868-7.539
54.501560919484-0.0425542310439570.377395400196368.10441490949681.19002327434484.87913093923210.223324307162670.14579999114457-0.077190.276305536941110.0684082648768311.612356310.32153900518453-1.0710409116974-0.232255190.40049007574286-0.0919965210290530.0186837360621890.527745827235210.258730348430330.73749805981277-46.11-42.9356.322
64.91173341642862.94861242411864.77632445196796.32390568380992.70202273257424.6504601040199-0.496958000297320.34812113522059-0.59211343-0.0378287944166910.0261418958663071.16179-0.00047325358358506-0.0240538230139040.40.40620593271227-0.037063740728934-0.0782072421087680.32474414575510.0263797016888980.50323231402418-29.198-31.5871.823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 53:172 )A53 - 172
2X-RAY DIFFRACTION2( CHAIN A AND RESID 173:295 )A173 - 295
3X-RAY DIFFRACTION3( CHAIN A AND RESID 296:329 )A296 - 329
4X-RAY DIFFRACTION4( CHAIN A AND RESID 330:396 )A330 - 396
5X-RAY DIFFRACTION5( CHAIN A AND RESID 397:416 )A397 - 416
6X-RAY DIFFRACTION6( CHAIN A AND RESID 501:501 )A501

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