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- PDB-3td9: Crystal structure of a Leucine binding protein LivK (TM1135) from... -

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Basic information

Entry
Database: PDB / ID: 3td9
TitleCrystal structure of a Leucine binding protein LivK (TM1135) from Thermotoga maritima MSB8 at 1.90 A resolution
ComponentsBranched chain amino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / leucine binding / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


: / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / Branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Leucine binding protein LivK (TM1135) from Thermotoga maritima MSB8 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Other
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,28314
Polymers40,3391
Non-polymers94413
Water4,720262
1
A: Branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules

A: Branched chain amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,56528
Polymers80,6772
Non-polymers1,88826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area2030 Å2
ΔGint-6 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.685, 91.315, 90.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Branched chain amino acid ABC transporter, periplasmic amino acid-binding protein


Mass: 40338.684 Da / Num. of mol.: 1 / Fragment: UNP residues 21-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1135, TM_1135 / Plasmid: MH2T7a / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9X0L9
#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. THE RESIDUES 5-20 WERE DELETED ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. THE RESIDUES 5-20 WERE DELETED FROM THE THE CONSTRUCT TO REMOVE A PREDICTED TRANSMEMBRANE REGION.

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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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.00% polyethylene glycol 400, 2.00M ammonium sulfate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.97921
ReflectionResolution: 1.9→29.7 Å / Num. all: 28707 / Num. obs: 28707 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.102 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.954.10.7032.2856420750.703100
1.95-24.10.5511.4841120400.551100
2-2.064.10.4731.6826320030.473100
2.06-2.124.10.3921.9800719420.392100
2.12-2.194.10.322.4766518540.32100
2.19-2.274.10.282.7748918160.28100
2.27-2.364.10.2333.3728417630.233100
2.36-2.454.10.2123.6701316970.212100
2.45-2.564.10.1734.4670016230.173100
2.56-2.694.10.1544.9640815510.154100
2.69-2.834.10.1285.9616814920.128100
2.83-34.10.1146.6578414040.114100
3-3.214.10.0937.9543813190.093100
3.21-3.474.10.0719.7508312390.071100
3.47-3.84.10.05711.5465211390.057100
3.8-4.254.10.04913.8422510420.049100
4.25-4.9140.04315.737239230.043100
4.91-6.0140.04813.431697920.048100
6.01-8.53.90.04814.124666310.048100
8.5-29.73.60.03714.713073620.03797.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.7 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.781 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.125
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. SULFATE ION (SO4) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 1450 5.1 %RANDOM
Rwork0.1508 ---
obs0.1529 28684 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.4 Å2 / Biso mean: 24.934 Å2 / Biso min: 11.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--1.47 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2669 0 61 262 2992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222840
X-RAY DIFFRACTIONr_bond_other_d0.0010.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9693839
X-RAY DIFFRACTIONr_angle_other_deg0.9234746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07325128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11115479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0631514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02559
X-RAY DIFFRACTIONr_mcbond_it0.691.51773
X-RAY DIFFRACTIONr_mcbond_other0.2061.5725
X-RAY DIFFRACTIONr_mcangle_it1.23422859
X-RAY DIFFRACTIONr_scbond_it2.23831067
X-RAY DIFFRACTIONr_scangle_it3.6774.5969
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 108 -
Rwork0.231 1962 -
all-2070 -
obs--99.95 %
Refinement TLS params.Method: refined / Origin x: 11.945 Å / Origin y: 31.499 Å / Origin z: 8.816 Å
111213212223313233
T0.0188 Å20.0132 Å20.0043 Å2-0.0084 Å20.0031 Å2--0.0593 Å2
L0.6029 °2-0.1164 °2-0.0148 °2-0.3648 °20.0768 °2--0.9432 °2
S0.0179 Å °0.0208 Å °-0.027 Å °0.0233 Å °-0.0187 Å °0.0108 Å °0.0407 Å °0.0541 Å °0.0007 Å °

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