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- PDB-4l8o: Crystal structure of a bile-acid 7-alpha dehydratase (CLOHYLEM_06... -

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Basic information

Entry
Database: PDB / ID: 4l8o
TitleCrystal structure of a bile-acid 7-alpha dehydratase (CLOHYLEM_06634) from Clostridium hylemonae DSM 15053 at 2.20 A resolution
ComponentsBile acid 7a-dehydratase, BaiE
KeywordsLYASE / SnoaL-like domain / PF13577 family protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


bile-acid 7alpha-dehydratase / bile-acid 7alpha-dehydratase activity
Similarity search - Function
SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium hylemonae DSM 15053 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a bile-acid 7-alpha dehydratase (CLOHYLEM_06634) from Clostridium hylemonae DSM 15053 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile acid 7a-dehydratase, BaiE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6448
Polymers22,2171
Non-polymers4267
Water1,26170
1
A: Bile acid 7a-dehydratase, BaiE
hetero molecules

A: Bile acid 7a-dehydratase, BaiE
hetero molecules

A: Bile acid 7a-dehydratase, BaiE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,93124
Polymers66,6523
Non-polymers1,27921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11140 Å2
ΔGint-124 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.956, 52.956, 428.627
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

CO

21A-202-

NA

31A-203-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bile acid 7a-dehydratase, BaiE


Mass: 22217.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium hylemonae DSM 15053 (bacteria)
Gene: baiE, CLOHYLEM_06634 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B4YSU1, bile-acid 7alpha-dehydratase

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Non-polymers , 5 types, 77 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (RESIDUES 1-169) 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: 2.6 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01M cobalt chloride, 1.80M ammonium sulfate, 0.1M MES pH 6.5, Additive - 0.001 M 3-oxo-delta 4,6, Lithocholyl Coenzyme A, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999941
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999941 Å / Relative weight: 1
ReflectionResolution: 2.2→28.575 Å / Num. obs: 12340 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.357 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.284.80.4792.95216109294.1
2.28-2.366.40.6437390114899.9
2.36-2.466.60.4983.973101108100
2.46-2.576.60.4014.970341067100
2.57-2.76.60.2896.768501035100
2.7-2.846.60.2268.66299956100
2.84-3.016.60.15512.16069926100
3.01-3.226.50.10417.4579588799.9
3.22-3.486.50.06825.85352824100
3.48-3.816.40.05231.6488075899.7
3.81-4.266.30.04139.14343690100
4.26-4.926.20.03246.33801616100
4.92-6.0360.03738.5329454599.9
6.03-8.525.80.03141.12500429100
8.52-28.585.30.01853.7136525997

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEMarch 15, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L8P

4l8p


Resolution: 2.2→28.575 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 9.914 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. COBALT (CO+2) IS MODELED BASED ON A PEAK IN THE ANOMALOUS DIFFERENCE FOURIER AND ITS PRESCIENCE IN THE CRYSTALLIZATION CONDITIONS. 6. THE MODELED ETHYLENE GLYCOL (EDO), SULFATE (SO4) AND SODIUM IONS (NA) ARE PRESENT IN CRYO / CRYSTALLIZATION / PROTEIN BUFFER SOLUTIONS. 7. RESIDUES IN THE LOOP FROM 55-57 ALONG WITH PART OF THE NEIGHBORING RESIDUES 54 AND 58 HAVE BEEN LEFT UNMODELED. THIS LOOP IS NEAR A CRYSTALLOGRAPHIC 3-FOLD AXIS AND IT WAS DIFFICULT TO BUILD THE MULTIPLE CONFORMATIONS REQUIRED TO FIT THE DENSITY AND AVOID A SYMMETRY CLASH. 8. THE SCATTERING FACTORS FOR SODIUM, SULFUR, AND COBALT ATOMS WERE ADJUSTED BY REFMAC 5.7.0032 TO ACCOUNT FOR ANOMALOUS DISPERSION BASED ON THE WAVELENGTH 1.000 A (NA F'=0.06, S F'=0.18, CO F'=0.15). THE CROMER MANN VALUES LISTED IN THE CIF VERSION OF THE FILE INCLUDE THIS CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 568 4.8 %RANDOM
Rwork0.1942 ---
obs0.1958 11786 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 103.21 Å2 / Biso mean: 35.1609 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.11 Å20 Å2
2--0.11 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 23 70 1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221409
X-RAY DIFFRACTIONr_bond_other_d0.0020.021319
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9691894
X-RAY DIFFRACTIONr_angle_other_deg0.84933063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97924.68864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71215265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.092155
X-RAY DIFFRACTIONr_chiral_restr0.0790.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
X-RAY DIFFRACTIONr_mcbond_it2.4543.548667
X-RAY DIFFRACTIONr_mcbond_other2.4043.55667
X-RAY DIFFRACTIONr_mcangle_it3.8826.581835
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.504 28 -
Rwork0.531 515 -
all-543 -
obs--61.77 %
Refinement TLS params.Method: refined / Origin x: 6.7007 Å / Origin y: 11.3469 Å / Origin z: 42.0699 Å
111213212223313233
T0.0535 Å2-0.0167 Å2-0.0021 Å2-0.032 Å2-0.0008 Å2--0.0918 Å2
L1.5941 °20.0734 °20.0094 °2-1.7673 °2-0.2136 °2--1.4446 °2
S-0.0475 Å °0.0603 Å °0.14 Å °-0.1123 Å °-0.0122 Å °-0.1014 Å °-0.085 Å °0.0806 Å °0.0597 Å °

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