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- PDB-4l8p: Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_0007... -

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Basic information

Entry
Database: PDB / ID: 4l8p
TitleCrystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.60 A resolution
ComponentsBile acid 7a-dehydratase, BaiE
KeywordsLYASE / Cystatin-like / 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 / metal ion binding
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
NICKEL (II) ION / TRIETHYLENE GLYCOL / Bile acid 7-alpha dehydratase
Similarity search - Component
Biological speciesClostridium hiranonis DSM 13275 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.60 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.pdbx_leaving_atom_flag / _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 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,7575
Polymers22,2871
Non-polymers4704
Water2,234124
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)68,27115
Polymers66,8613
Non-polymers1,41012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area10990 Å2
ΔGint-94 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.905, 58.905, 91.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21A-202-

NA

31A-421-

HOH

41A-422-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 22287.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium hiranonis DSM 13275 (bacteria)
Gene: baiE, CLOHIR_00079 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9RB47, bile-acid 7alpha-dehydratase

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 1-168) 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50.00% polyethylene glycol 200, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 23, 2010
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.6→29.452 Å / Num. all: 23715 / Num. obs: 23715 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.737 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.6470.6512.71217417430.651100
1.64-1.697.10.57831191816800.578100
1.69-1.747.20.473.61195316630.47100
1.74-1.797.20.3834.31174416260.383100
1.79-1.857.30.31851128415560.318100
1.85-1.917.30.2765.81096115060.276100
1.91-1.987.20.27.41059214650.2100
1.98-2.077.30.1639.21011713840.163100
2.07-2.167.30.15510.8994013570.155100
2.16-2.267.30.14112.1948713020.141100
2.26-2.397.40.12413.7891812040.124100
2.39-2.537.40.12114.2867711750.121100
2.53-2.77.40.10715.8804310890.107100
2.7-2.927.40.08718.2757410200.087100
2.92-3.27.40.06720.769539340.067100
3.2-3.587.40.05725.662328410.057100
3.58-4.137.40.05828.456167580.058100
4.13-5.067.40.05129.247396390.051100
5.06-7.167.30.06124.936284950.061100
7.16-29.4527.10.05826.319632780.05897.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→29.452 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 3.062 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. 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. A NICKEL ION (NI+2) IS MODELED BASED ON A PEAK IN THE ANOMALOUS DIFFERENCE FOURIER. X-RAY FLUORESCENCE EMISSION SPECTRA SHOWED PEAKS CORRESPONDING TO THE NICKEL AND ZINC K-EDGES. DATA SETS WERE COLLECTED ABOVE AND BELOW THE ZINC AND NICKEL K-EDGES. COMPARING ANOMALOUS DIFFERENCE FOURIER MAPS FROM THESE 4 DATA SETS SUGGESTS A MIXTURE WITH MORE NICKEL THAN ZINC. 7. THE MODELED PEG 200 FRAGMENTS (1PE AND PGE) AND SODIUM IONS ARE PRESENT IN THE CRYSTALLIZATION SOLUTION AND PROTEIN BUFFER. 8. THE SCATTERING FACTORS FOR SULFUR, SELENIUM AND ZINC ATOMS WERE ADJUSTED BY REFMAC 5.7.0032 TO ACCOUNT FOR ANOMALOUS DISPERSION. THE SELENIUM CORRECTION WAS DERIVED FROM THE X-RAY FLUORESCENCE MAD SCAN WITH CHOOCH. THE CORRECTIONS FOR NICKEL AND SULFUR WERE BASED ON THE WAVELENGTH 0.97945 A (S F'= 0.18, SE F'= -7.60, NI F'= 0.06). THE CROMER MANN VALUES LISTED IN THE CIF VERSION OF THE FILE INCLUDE THIS CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 1222 5.2 %RANDOM
Rwork0.1512 ---
obs0.1526 23680 99.93 %-
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: 96.87 Å2 / Biso mean: 24.7923 Å2 / Biso min: 12.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.73 Å2-0 Å2
2--0.73 Å2-0 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 28 124 1518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191465
X-RAY DIFFRACTIONr_bond_other_d0.0030.021369
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9831973
X-RAY DIFFRACTIONr_angle_other_deg0.89533174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40824.9371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03115241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.896156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021632
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02322
X-RAY DIFFRACTIONr_mcbond_it2.123.209695
X-RAY DIFFRACTIONr_mcbond_other2.1173.194694
X-RAY DIFFRACTIONr_mcangle_it3.2066.006874
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 96 -
Rwork0.234 1648 -
all-1744 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 12.958 Å / Origin y: 35.894 Å / Origin z: 5.255 Å
111213212223313233
T0.0248 Å2-0.0073 Å20.0089 Å2-0.0283 Å2-0.0021 Å2--0.0363 Å2
L0.3613 °2-0.0481 °20.1564 °2-0.4674 °2-0.0771 °2--0.5996 °2
S0.0007 Å °0.0389 Å °0.0171 Å °-0.0366 Å °0.0131 Å °-0.0779 Å °-0.0611 Å °0.093 Å °-0.0137 Å °

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