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- PDB-4kqc: ABC transporter, LacI family transcriptional regulator from Brach... -

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Basic information

Entry
Database: PDB / ID: 4kqc
TitleABC transporter, LacI family transcriptional regulator from Brachyspira murdochii
ComponentsPeriplasmic binding protein/LacI transcriptional regulator
KeywordsTRANSPORT PROTEIN / structural genomics / APC110243 / ABC transporter / solute-binding proteins / transcriptional regulator / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


cell envelope / carbohydrate binding / plasma membrane
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Periplasmic binding protein/LacI transcriptional regulator
Similarity search - Component
Biological speciesBrachyspira murdochii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.62 Å
AuthorsOsipiuk, J. / Joachimiak, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: ABC transporter, LacI family transcriptional regulator from Brachyspira murdochii
Authors: Osipiuk, J. / Joachimiak, G. / Clancy, S. / Joachimiak, A.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Oct 9, 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 / _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: Periplasmic binding protein/LacI transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3156
Polymers34,0051
Non-polymers3105
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.356, 59.241, 65.454
Angle α, β, γ (deg.)90.000, 102.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Periplasmic binding protein/LacI transcriptional regulator


Mass: 34005.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brachyspira murdochii (bacteria) / Strain: DSM 12563 / Gene: Bmur_2490 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5U661
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2 M nitrate sulfate, 20% PEG-3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.62→31.9 Å / Num. all: 35470 / Num. obs: 35470 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.103 / Χ2: 2.179 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.62-1.652.60.5342.1514771.10481.1
1.65-1.682.80.48616281.06289.1
1.68-1.713.10.46817341.17797
1.71-1.753.30.39417831.32397.4
1.75-1.783.50.36217951.47399.9
1.78-1.823.50.32718221.63899.6
1.82-1.873.50.29217791.91399.2
1.87-1.923.50.25518462.11599.1
1.92-1.983.50.20817782.19198.7
1.98-2.043.50.17817862.37898.7
2.04-2.113.50.16218092.63898.3
2.11-2.23.50.14417812.90598.2
2.2-2.33.50.12717702.72498.3
2.3-2.423.50.1218202.95498.7
2.42-2.573.50.11117932.70498.7
2.57-2.773.50.10118082.84398.6
2.77-3.053.50.0917892.56898.3
3.05-3.493.40.07818072.38397.4
3.49-4.43.40.06418132.00298.3
4.4-503.40.0618522.38197.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.62→31.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.193 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1883 1783 5 %RANDOM
Rwork0.1511 ---
all0.1529 35453 --
obs0.1529 35453 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.33 Å2 / Biso mean: 17.2356 Å2 / Biso min: 8.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20.27 Å2
2---0.87 Å2-0 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.62→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 20 379 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022587
X-RAY DIFFRACTIONr_bond_other_d0.0010.022493
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9683535
X-RAY DIFFRACTIONr_angle_other_deg0.85535781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6915365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88726.271118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09515447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9621510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
LS refinement shellResolution: 1.618→1.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 113 -
Rwork0.249 2074 -
all-2187 -
obs-2187 80.67 %
Refinement TLS params.Method: refined / Origin x: 6.6995 Å / Origin y: -19.7692 Å / Origin z: 14.7903 Å
111213212223313233
T0.0188 Å2-0.0014 Å20.0009 Å2-0.0281 Å2-0.001 Å2--0.0014 Å2
L0.085 °20.0961 °2-0.0872 °2-0.3238 °2-0.1618 °2--0.1599 °2
S0.0045 Å °-0.0046 Å °0.0076 Å °-0.0019 Å °-0.0027 Å °0.0091 Å °0.0015 Å °0.0022 Å °-0.0019 Å °

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