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

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Basic information

Entry
Database: PDB / ID: 2wuf
TitleCrystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis in complex with 4,9DSHA
Components2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE BPHD
KeywordsHYDROLASE
Function / homology
Function and homology information


4,9-DSHA hydrolase activity / 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 / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / 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
Chem-KEM / 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: 1.9 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 1.3Dec 19, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_symm_contact / struct_conn
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
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)64,3906
Polymers63,7992
Non-polymers5924
Water3,297183
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


Theoretical massNumber of molelcules
Total (without water)64,0996
Polymers63,7992
Non-polymers3004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x-1/2,y,-z+1/21
Buried area1720 Å2
ΔGint-7.12 kcal/mol
Surface area22890 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


Theoretical massNumber of molelcules
Total (without water)64,6826
Polymers63,7992
Non-polymers8834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area2110 Å2
ΔGint-14.7 kcal/mol
Surface area22450 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 7:209 OR RESSEQ 213:288 ))
211(CHAIN B AND (RESSEQ 7:209 OR RESSEQ 213:288 ))

NCS oper: (Code: given
Matrix: (0.025519, 0.999653, -0.006465), (0.999663, -0.025549, -0.00462), (-0.004783, -0.006345, -0.999968)
Vector: 30.9238, -30.9024, 44.9637)

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-KEM / (3E,5R)-8-[(1S,3AR,4R,7AS)-1-HYDROXY-7A-METHYL-5-OXOOCTAHYDRO-1H-INDEN-4-YL]-5-METHYL-2,6-DIOXOOCT-3-ENOATE


Mass: 349.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.33 Å3/Da / Density % sol: 47.28 % / 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: 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: 1.9→40.59 Å / Num. obs: 46107 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 99.3

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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: 1.9→40.59 Å / SU ML: 0.31 / σ(F): 2 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 2252 5.1 %
Rwork0.209 --
obs-42140 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.1 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 40 183 4593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d0.82
X-RAY DIFFRACTIONf_dihedral_angle_d11.16
X-RAY DIFFRACTIONf_chiral_restr0.071
X-RAY DIFFRACTIONf_plane_restr0.004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2257X-RAY DIFFRACTIONPOSITIONAL
12B2257X-RAY DIFFRACTIONPOSITIONAL0.618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94140.33371180.2532414X-RAY DIFFRACTION88
1.9414-1.98650.31561100.24452482X-RAY DIFFRACTION89
1.9865-2.03620.26461370.22442561X-RAY DIFFRACTION91
2.0362-2.09120.25661400.21892523X-RAY DIFFRACTION92
2.0912-2.15280.24531520.21032618X-RAY DIFFRACTION95
2.1528-2.22230.27881290.21322614X-RAY DIFFRACTION95
2.2223-2.30170.2411280.19892676X-RAY DIFFRACTION96
2.3017-2.39380.25541600.19672651X-RAY DIFFRACTION96
2.3938-2.50270.23881430.19672672X-RAY DIFFRACTION97
2.5027-2.63470.30491340.21562716X-RAY DIFFRACTION97
2.6347-2.79970.25441330.21922723X-RAY DIFFRACTION97
2.7997-3.01580.22731580.21542702X-RAY DIFFRACTION97
3.0158-3.31920.22851490.2122699X-RAY DIFFRACTION97
3.3192-3.79920.19311470.17492737X-RAY DIFFRACTION97
3.7992-4.78530.17121460.15752660X-RAY DIFFRACTION94
4.7853-40.59920.21841680.21922692X-RAY DIFFRACTION93
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)
10.78630.2254-0.10830.2269-0.21390.1460.16790.00840.0290.19070.02230.1281-13.653-16.551329.0404
20.136-0.1208-0.1860.4706-0.0560.49760.13-0.0602-0.06150.10110.03930.181113.153-44.721216.1311
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)

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