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

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Basic information

Entry
Database: PDB / ID: 2wud
TitleCrystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis
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 / chlorophyllase activity / 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 / chlorophyll metabolic process / biological process involved in interaction with host / steroid biosynthetic process / : ...4,9-DSHA hydrolase activity / 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase / chlorophyllase activity / 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 / chlorophyll metabolic process / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 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 1.5Dec 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)63,9154
Polymers63,7992
Non-polymers1162
Water4,954275
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)127,8308
Polymers127,5984
Non-polymers2324
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-30.96 kcal/mol
Surface area40130 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)127,8308
Polymers127,5984
Non-polymers2324
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 area9260 Å2
ΔGint-19.48 kcal/mol
Surface area40210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.254, 118.765, 182.592
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: (0.034051, 0.999419, 0.001446), (0.999372, -0.034035, -0.009898), (-0.009844, 0.001782, -0.99995)
Vector: 31.1624, -31.5206, 45.8312)

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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: 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: 2.45 Å3/Da / Density % sol: 49.9 % / 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 4, 2008 / Details: MONTEL 200 OPTICS
RadiationMonochromator: MONTEL 200 OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→59.8 Å / Num. obs: 35484 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 16.55 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VF2

2vf2


Resolution: 2.1→49.8 Å / SU ML: 0.3 / σ(F): 2 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1779 5 %
Rwork0.192 --
obs-35439 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.943 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso mean: 19.86 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 6 275 4651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.746
X-RAY DIFFRACTIONf_dihedral_angle_d10.285
X-RAY DIFFRACTIONf_chiral_restr0.066
X-RAY DIFFRACTIONf_plane_restr0.003
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2185X-RAY DIFFRACTIONPOSITIONAL
12B2185X-RAY DIFFRACTIONPOSITIONAL0.311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15680.29361260.23582542X-RAY DIFFRACTION99
2.1568-2.22030.27191380.23462568X-RAY DIFFRACTION100
2.2203-2.29190.29091370.22962573X-RAY DIFFRACTION100
2.2919-2.37380.28461410.21842580X-RAY DIFFRACTION100
2.3738-2.46890.26581330.21272576X-RAY DIFFRACTION100
2.4689-2.58120.28411400.20652568X-RAY DIFFRACTION100
2.5812-2.71730.25291420.21182582X-RAY DIFFRACTION99
2.7173-2.88750.22881350.20642569X-RAY DIFFRACTION99
2.8875-3.11050.26581590.18082574X-RAY DIFFRACTION100
3.1105-3.42340.23491470.17582590X-RAY DIFFRACTION100
3.4234-3.91860.19291360.15722616X-RAY DIFFRACTION100
3.9186-4.93630.1441120.14082659X-RAY DIFFRACTION100
4.9363-49.79290.1931330.17762663X-RAY DIFFRACTION97
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)
10.92630.2766-0.45681.60730.11031.18580.0808-0.05890.00370.15830.02240.098-8.9639-7.4317.273
21.04990.6237-0.35861.0539-0.3350.19310.093-0.03630.00550.09640.01530.1026-10.8419-14.927322.1954
30.7669-0.0857-0.15780.2461-0.25680.82840.0905-0.029-0.00960.0727-0.00610.0908-18.6005-11.529231.8675
40.374-0.4941-0.08360.78340.06270.19710.0823-0.02030.01540.16990.02520.16130.5303-23.995333.9934
53.41741.2881-6.06320.0733-1.36895.65440.1369-0.0361-0.07450.25150.08890.1554-5.1638-8.05642.2106
60.82720.19240.4337-0.09580.9321.80240.1319-0.0373-0.00640.12320.03010.07-24.4819-9.098640.8924
70.06260.19550.22960.8472-0.36350.53430.0693-0.02340.00650.0797-0.00120.0447-22.2256-25.825829.8621
82.2370.0273-0.3131.50320.88932.780.07960.0047-0.08340.217-0.12590.178622.7854-41.591728.4007
91.64-0.01930.8301-0.22050.6570.66990.1071-0.0002-0.03440.1475-0.08820.214215.3507-42.219423.1758
100.393-0.52960.39730.10560.2560.5240.0923-0.0287-0.00960.13250.00880.138818.4273-50.411913.712
110.6389-0.0967-0.1706-0.51650.6580.36170.2031-0.0333-0.01960.06080.00410.2126.5975-30.904411.7318
120.2036-0.3548-3.32-1.9329.32031.34120.63050.0809-0.12010.501-0.06770.351222.0426-37.28783.2148
130.71080.1535-0.73790.97570.08290.61730.1009-0.0218-0.01570.17990.02040.085720.5649-56.34544.6993
141.058-0.09390.28810.3670.06490.22780.058-0.0239-0.01240.097-0.00180.0524.0307-53.579315.8107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:36)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 37:84)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 85:156)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 157:205)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 206:213)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 214:230)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 231:288)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 7:37)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 38:84)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 85:156)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 157:205)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 206:213)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 214:230)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 231:288)

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