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- PDB-2wue: Crystal structure of S114A mutant of HsaD from Mycobacterium tube... -

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Basic information

Entry
Database: PDB / ID: 2wue
TitleCrystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis in complex with HOPODA
Components2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
KeywordsHYDROLASE
Function / homology
Function and homology information


4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase activity / : / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances / steroid biosynthetic process / biological process involved in interaction with host / lipid catabolic process / peptidoglycan-based cell wall / plasma membrane
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KEK / THIOCYANATE ION / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLack, N.A. / Yam, K.C. / Lowe, E.D. / Horsman, G.P. / Owen, R. / Sim, E. / Eltis, L.D.
CitationJournal: J. Biol. Chem. / Year: 2010
Title: Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism.
Authors: Lack, N.A. / Yam, K.C. / Lowe, E.D. / Horsman, G.P. / Owen, R.L. / Sim, E. / Eltis, L.D.
History
DepositionOct 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2095
Polymers63,7992
Non-polymers4103
Water6,017334
1
A: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules

A: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules

A: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules

A: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,06212
Polymers127,5984
Non-polymers4658
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x-1/2,y,-z+1/21
crystal symmetry operation8_545x,-y-1/2,-z+1/21
crystal symmetry operation14_445-x-1/2,-y-1/2,z1
Buried area9210 Å2
ΔGint-22.78 kcal/mol
Surface area40220 Å2
MethodPISA
2
B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules

B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules

B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules

B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7728
Polymers127,5984
Non-polymers1,1754
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area8860 Å2
ΔGint-22.57 kcal/mol
Surface area38960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.883, 117.971, 180.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-2056-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 7:200 OR RESSEQ 214:288 ))
211(CHAIN B AND (RESSEQ 7:200 OR RESSEQ 214:288 ))

NCS oper: (Code: given
Matrix: (0.031368, 0.999502, -0.003362), (0.99949, -0.031388, -0.005939), (-0.006041, -0.003174, -0.999977)
Vector: 30.8241, -31.1847, 45.1163)

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Components

#1: Protein 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD / HSAD / 2-HYDROXY-6-PHENYLHEXA-2\ / 4-DIENOIC ACID HYDROLASE


Mass: 31899.389 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PT7-7 / Production host: Escherichia coli DH5[alpha] (bacteria)
References: UniProt: P96851, UniProt: P9WNH5*PLUS, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-KEK / (3E,5R)-8-(2-CHLOROPHENYL)-5-METHYL-2,6-DIOXOOCT-3-ENOATE


Mass: 293.722 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14ClO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 114 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 114 TO ALA
Sequence detailsS114A MUTANT

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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: 2.35 Å3/Da / Density % sol: 47.63 % / Description: NONE
Crystal growpH: 7
Details: 200MM KSCN, 24% PET 3350, 100MM BIS-TRIS PROPANE PH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9757
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 22, 2008
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 1.8→40.66 Å / Num. obs: 55043 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUD

2wud


Resolution: 1.8→36.34 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 2716 5.1 %
Rwork0.194 --
obs-53203 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.28 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 26 334 4734
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.716
X-RAY DIFFRACTIONf_dihedral_angle_d10.4
X-RAY DIFFRACTIONf_chiral_restr0.062
X-RAY DIFFRACTIONf_plane_restr0.004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2122X-RAY DIFFRACTIONPOSITIONAL
12B2122X-RAY DIFFRACTIONPOSITIONAL0.64591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.794-1.82660.30731180.26772288X-RAY DIFFRACTION82
1.8266-1.86170.26871360.25322466X-RAY DIFFRACTION90
1.8617-1.89970.26471390.23382535X-RAY DIFFRACTION91
1.8997-1.9410.25741360.22892541X-RAY DIFFRACTION93
1.941-1.98620.24521550.22362600X-RAY DIFFRACTION94
1.9862-2.03590.22771530.20842664X-RAY DIFFRACTION96
2.0359-2.09090.2361260.21062668X-RAY DIFFRACTION96
2.0909-2.15240.23331410.20592687X-RAY DIFFRACTION97
2.1524-2.22190.22561440.20312664X-RAY DIFFRACTION97
2.2219-2.30130.22111430.19622723X-RAY DIFFRACTION98
2.3013-2.39340.21881530.19462733X-RAY DIFFRACTION98
2.3934-2.50230.20911420.19782704X-RAY DIFFRACTION98
2.5023-2.63420.2461480.20882741X-RAY DIFFRACTION98
2.6342-2.79920.23171490.20292734X-RAY DIFFRACTION98
2.7992-3.01520.20471610.19292718X-RAY DIFFRACTION98
3.0152-3.31850.21411670.19062705X-RAY DIFFRACTION98
3.3185-3.79820.16341400.172774X-RAY DIFFRACTION98
3.7982-4.78360.14681270.15432742X-RAY DIFFRACTION96
4.7836-36.34980.19241380.18352800X-RAY DIFFRACTION95
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42030.087-0.08880.322-0.16520.09640.1259-0.03610.00470.119-0.00570.0978-13.9414-16.719228.7492
20.2797-0.4004-0.20590.3984-0.09930.44490.1218-0.0598-0.03420.1364-0.0040.158913.073-44.991516.475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)

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