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- PDB-4lgc: Crystal structure of a bile acid-coenzyme A ligase (baiB) from Cl... -

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Basic information

Entry
Database: PDB / ID: 4lgc
TitleCrystal structure of a bile acid-coenzyme A ligase (baiB) from Clostridium scindens (VPI 12708) at 2.19 A resolution
ComponentsBile acid-coenzyme A ligase
KeywordsLIGASE / ATP-dependent AMP-binding enzyme family / lipoprotein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


cholate-CoA ligase / cholate-CoA ligase activity / bile acid catabolic process / bile acid biosynthetic process / lipid catabolic process / ATP binding / cytoplasm
Similarity search - Function
: / : / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily ...: / : / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bile acid--coenzyme A ligase
Similarity search - Component
Biological speciesClostridium scindens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a bile acid-coenzyme A ligase (baiB) from Clostridium scindens (VPI 12708) at 2.19 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bile acid-coenzyme A ligase


Theoretical massNumber of molelcules
Total (without water)61,5701
Polymers61,5701
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.819, 86.320, 95.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bile acid-coenzyme A ligase


Mass: 61569.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium scindens (bacteria) / Strain: VPI 12708 / Gene: BA20564A, baiB / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: P19409, Ligases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 1-520) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20.00% Ethanol, 0.1M TRIS pH 8.5, Additive - 0.001 M cholic acid, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 14, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.19→45.88 Å / Num. obs: 28363 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 43.297 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.11
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.19-2.270.9531.9153122634190.8
2.27-2.360.7842.51698727611100
2.36-2.470.633.31773828851100
2.47-2.60.5064.41722127891100
2.6-2.760.3696.11727927921100
2.76-2.970.2278.71737128181100
2.97-3.270.13912.31747628531100
3.27-3.740.08317.2172322878199.9
3.74-4.70.06121167382882199.7
4.7-45.880.06621.7167023071198.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→45.88 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.562 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.175
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. A MET- ...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. 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. 5. THE C-TERMINAL DOMAIN (416-520) IS LIKELY DISORDERED IN THE CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1430 5.1 %RANDOM
Rwork0.1886 ---
obs0.1906 28254 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.71 Å2 / Biso mean: 47.8071 Å2 / Biso min: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å2-0 Å2-0 Å2
2---0.77 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.19→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 0 73 3142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193159
X-RAY DIFFRACTIONr_bond_other_d0.0010.022961
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9784281
X-RAY DIFFRACTIONr_angle_other_deg0.80936848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0925396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78224.444135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21515491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7641513
X-RAY DIFFRACTIONr_chiral_restr0.0880.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02706
X-RAY DIFFRACTIONr_mcbond_it2.6653.7611575
X-RAY DIFFRACTIONr_mcbond_other2.6633.7581574
X-RAY DIFFRACTIONr_mcangle_it3.8635.6271965
LS refinement shellResolution: 2.193→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 101 -
Rwork0.319 1774 -
all-1875 -
obs--91.2 %
Refinement TLS params.Method: refined / Origin x: 15.8665 Å / Origin y: -4.3919 Å / Origin z: -3.5469 Å
111213212223313233
T0.0187 Å20.0016 Å2-0.0069 Å2-0.0069 Å20.0022 Å2--0.0231 Å2
L0.3521 °20.1094 °2-0.0818 °2-0.9185 °20.163 °2--1.35 °2
S-0.0127 Å °-0.0494 Å °-0.0152 Å °-0.0643 Å °-0.0139 Å °0.0481 Å °-0.1431 Å °0.0131 Å °0.0266 Å °

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