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

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Basic information

Entry
Database: PDB / ID: 2wug
TitleCrystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis in complex with HOPDA
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 carbon-carbon bonds, in ketonic substances / biological process involved in interaction with host / steroid biosynthetic process / 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
(3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE / 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.L. / Sim, E. / Eltis, L.D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Characterization of a C-C Hydrolase from Mycobacterium Tuberuclosis 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 1.3Dec 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)64,3836
Polymers63,7992
Non-polymers5854
Water4,954275
1
A: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1753
Polymers31,8991
Non-polymers2752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2093
Polymers31,8991
Non-polymers3092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

NCS oper: (Code: given
Matrix: (0.025482, 0.999643, -0.007984), (0.999668, -0.025512, -0.003644), (-0.003847, -0.007889, -0.999961)
Vector: 30.8648, -30.864, 44.8384)

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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 (E. coli) / Strain (production host): DH5[ALPHA]
References: UniProt: P96851, UniProt: P9WNH5*PLUS, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
#2: Chemical ChemComp-HPK / (3E)-2,6-DIOXO-6-PHENYLHEX-3-ENOATE


Mass: 217.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9O4
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.36 Å3/Da / Density % sol: 48.01 % / Description: NONE
Crystal growpH: 7
Details: 200MM KSCN, 24% PEG 3350, 100MM BIS-TRIS PROPANE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2008 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.8→29.49 Å / Num. obs: 55165 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 16.5 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→29.49 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 16.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.167 2730 5 %
Rwork0.192 --
obs-54360 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.68 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 41 275 4694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.774
X-RAY DIFFRACTIONf_dihedral_angle_d10.42
X-RAY DIFFRACTIONf_chiral_restr0.063
X-RAY DIFFRACTIONf_plane_restr0.005
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2249X-RAY DIFFRACTIONPOSITIONAL
12B2249X-RAY DIFFRACTIONPOSITIONAL0.527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7823-1.81470.2242980.19771828X-RAY DIFFRACTION65
1.8147-1.84960.24621460.18642651X-RAY DIFFRACTION94
1.8496-1.88730.20261320.17662681X-RAY DIFFRACTION95
1.8873-1.92830.22651420.17422694X-RAY DIFFRACTION95
1.9283-1.97320.19661690.17122644X-RAY DIFFRACTION95
1.9732-2.02250.20281560.15772721X-RAY DIFFRACTION97
2.0225-2.07720.18191280.16432762X-RAY DIFFRACTION97
2.0772-2.13830.17821500.16042764X-RAY DIFFRACTION97
2.1383-2.20730.20011380.15942732X-RAY DIFFRACTION97
2.2073-2.28610.19261370.15352756X-RAY DIFFRACTION97
2.2861-2.37760.1581190.15422777X-RAY DIFFRACTION97
2.3776-2.48570.19191540.15082772X-RAY DIFFRACTION98
2.4857-2.61670.22031510.16392796X-RAY DIFFRACTION98
2.6167-2.78050.19631360.17572776X-RAY DIFFRACTION98
2.7805-2.9950.20511590.17592810X-RAY DIFFRACTION99
2.995-3.2960.21161470.17552833X-RAY DIFFRACTION99
3.296-3.77190.18111570.15522814X-RAY DIFFRACTION99
3.7719-4.74850.15351500.1452863X-RAY DIFFRACTION99
4.7485-28.04310.18991610.17942956X-RAY DIFFRACTION99
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)
10.4296-0.0502-0.08140.316-0.09430.19280.0444-0.03560.00030.0620.00340.0348-13.7086-16.514529.2109
20.3093-0.3139-0.16150.34260.03910.49870.0838-0.0488-0.03190.05810.00920.090713.3215-44.737115.9484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)

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