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- PDB-4n3v: Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_0007... -

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Basic information

Entry
Database: PDB / ID: 4n3v
TitleCrystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.89 A resolution with product added
ComponentsBile acid 7-alpha dehydratase, BaiE
KeywordsLYASE / SnoaL-like domain / PF13577 family / 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
CITRIC ACID / Unknown ligand / Bile acid 7-alpha dehydratase
Similarity search - Component
Biological speciesClostridium hiranonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 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 1.89 A resolution with product added
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,77912
Polymers43,9182
Non-polymers86110
Water3,405189
1
A: Bile acid 7-alpha dehydratase, BaiE
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)67,61921
Polymers65,8763
Non-polymers1,74318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11070 Å2
ΔGint-122 kcal/mol
Surface area23590 Å2
MethodPISA
2
B: Bile acid 7-alpha dehydratase, BaiE
hetero molecules

B: Bile acid 7-alpha dehydratase, BaiE
hetero molecules

B: Bile acid 7-alpha dehydratase, BaiE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,71815
Polymers65,8763
Non-polymers84212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area12520 Å2
ΔGint-142 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.282, 84.282, 311.823
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

21A-202-

NA

31A-203-

CIT

41A-203-

CIT

51B-201-

ZN

61B-202-

NA

71B-203-

CIT

81B-203-

CIT

91A-378-

HOH

101B-409-

HOH

111B-410-

HOH

121B-411-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: UNL / End label comp-ID: UNL / Refine code: _ / Auth seq-ID: 0 - 180 / Label seq-ID: 19

Dom-IDEnd label alt-IDAuth asym-IDLabel asym-ID
1AAA - H
2BBB - I

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 21958.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium hiranonis (bacteria) / Strain: DSM 13275 / Gene: baiE, CLOHIR_00079 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q9RB47, bile-acid 7alpha-dehydratase

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Non-polymers , 7 types, 199 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10.00% polyethylene glycol 6000, 0.1M citric acid pH 5.0, 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: 0.999947
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: 0.999947 Å / Relative weight: 1
ReflectionResolution: 1.89→47.414 Å / Num. obs: 34715 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.185 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.073 / Net I/σ(I): 19.5 / Num. measured all: 362385
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.89-1.947.20.8852.51789124860.350.95398.8
1.94-1.999.50.6233.92336424660.2110.658100
1.99-2.05110.4515.72676524320.1420.473100
2.05-2.11110.3487.12549123140.1090.365100
2.11-2.18110.2598.92507822780.0810.272100
2.18-2.26110.2319.92400821850.0730.242100
2.26-2.34110.18511.72357221420.0580.194100
2.34-2.44110.16512.92229120290.0520.173100
2.44-2.55110.13814.92184419920.0440.145100
2.55-2.6710.90.11517.52027118540.0360.1299.9
2.67-2.8210.90.09121.51962318040.0290.095100
2.82-2.9910.80.07325.21832516890.0230.076100
2.99-3.1910.70.05831.11723816080.0190.061100
3.19-3.4510.50.04937.41576115000.0160.051100
3.45-3.7810.30.04144.71412413770.0130.043100
3.78-4.2310.30.03647.51299012670.0120.038100
4.23-4.8810.50.03253.31170911180.010.033100
4.88-5.9810.50.03348.999709540.0110.035100
5.98-8.4510.30.0314878957690.010.033100
8.45-47.419.30.02551.741724500.0080.02699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4l8p


Resolution: 1.89→47.414 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 5.543 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.129 / 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. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED IN A POCKET FORMED BY PROTOMERS FROM TWO ADJACENT TRIMERS IN THE CRYSTAL LATTICE. THIS UNL MAY REPRESENT THE ADDED PRODUCT COMPOUND, 3-OXO-DELTA 4,6, LITHOCHOLYL COENZYME A. HOWEVER, THE 2-FOLD DISORDER OF THE SITE AND LIKELY PARTIAL OCCUPANCY PREVENTS DEFANITIVIE ASSIGNEMNT OF THESE DENSITY FEATURES. 6. A ZINC ION (ZN2+) IS MODELED BASED ON A PEAK IN THE ANOMALOUS DIFFERENCE FOURIER MAP. THE ZINC ASSIGNMENT WAS TENATIVLY BASED ON THE PRESENCE OF ENDOGENOUS ZINC IN A HOMOLOG STRUCTURE AND COULD REPRESENT A DIFFERENT METAL ION. X-RAY FLUORESCENCE SPECTRA WERE NOT AVAILABLE FOR THIS CRYSTAL. 7. THE MODELED CITRIC ACID (CIT), PEG FRAGMENT (1PE), 1,2- ETHANEDIOL AND SODIUM ION (NA1+) ARE PRESENT IN THE CRYSTALLIZATION SOLUTION, CRYO SOLUTION AND PROTEIN BUFFER. 8. THE SCATTERING FACTORS FOR SODIUM, SULFUR, AND ZINC ATOMS WERE ADJUSTED BY REFMAC 5.7.0032 TO ACCOUNT FOR ANOMALOUS DISPERSION BASED ON THE WAVELENGTH 0.9999 A (NA F'= 0.06, S F'= 0.19, ZN F'= -0.35). THE CROMER MANN VALUES LISTED IN THE CIF VERSION OF THE FILE INCLUDE THIS CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1748 5 %RANDOM
Rwork0.1879 32963 --
obs0.1894 34711 99.87 %-
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: 108.78 Å2 / Biso mean: 35.823 Å2 / Biso min: 15.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.55 Å20 Å2
2--0.55 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 1.89→47.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 124 189 3035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193001
X-RAY DIFFRACTIONr_bond_other_d0.0030.022700
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9144071
X-RAY DIFFRACTIONr_angle_other_deg0.82336261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3485354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12724.898147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19415524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4361512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023338
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02662
X-RAY DIFFRACTIONr_mcbond_it3.3344.2751371
X-RAY DIFFRACTIONr_mcbond_other3.3184.2711370
X-RAY DIFFRACTIONr_mcangle_it4.3727.9421722
Refine LS restraints NCS

Ens-ID: 1 / Number: 24935 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 108 -
Rwork0.259 2363 -
all-2471 -
obs--98.68 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4517-0.15580.49921.3094-0.40380.58710.01650.03710.13930.00410.05540.1684-0.1368-0.1021-0.07190.06890.040.03030.04630.02360.069434.843335.5881138.3082
21.28390.1644-0.29091.0744-0.15370.7790.0303-0.0788-0.1190.03050.0360.11790.0746-0.0767-0.06640.0224-0.0109-0.01430.01840.02150.073635.069561.6281117.7408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 166
2X-RAY DIFFRACTION2B0 - 166

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