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- PDB-4wnb: Crystal structure of the ChsH1-ChsH2 complex from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 4wnb
TitleCrystal structure of the ChsH1-ChsH2 complex from Mycobacterium tuberculosis bound to 3-OPC-CoA
Components
  • Hydratase ChsH1
  • Hydratase ChsH2
KeywordsLYASE
Function / homologyHotdog Thioesterase / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta / 3-oxo-4-pregnene-20-carboxyl-Coenzyme A / : / : / :
Function and homology information
Biological speciesMycobacterium tuberculosis KZN 4207 (bacteria)
Mycobacterium tuberculosis C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGuja, K.E. / Yang, M. / Sampson, N. / Garcia-Diaz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM100021 United States
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: A Distinct MaoC-like Enoyl-CoA Hydratase Architecture Mediates Cholesterol Catabolism in Mycobacterium tuberculosis.
Authors: Yang, M. / Guja, K.E. / Thomas, S.T. / Garcia-Diaz, M. / Sampson, N.S.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionOct 29, 2014ID: 4W7B
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydratase ChsH2
B: Hydratase ChsH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5396
Polymers34,1802
Non-polymers1,3594
Water4,774265
1
A: Hydratase ChsH2
B: Hydratase ChsH1
hetero molecules

A: Hydratase ChsH2
B: Hydratase ChsH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,07712
Polymers68,3604
Non-polymers2,7188
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area9080 Å2
ΔGint-80 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.882, 51.882, 436.235
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21B-314-

HOH

31B-318-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hydratase ChsH2


Mass: 20213.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis KZN 4207 (bacteria)
Gene: TBSG_03608, V459_03372 / Production host: Escherichia coli (E. coli) / References: UniProt: I1SFB1
#2: Protein Hydratase ChsH1


Mass: 13965.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis C (bacteria)
Gene: TBCG_03470 / Production host: Escherichia coli (E. coli) / References: UniProt: A2VPV3

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Non-polymers , 4 types, 269 molecules

#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-4BN / 3-oxo-4-pregnene-20-carboxyl-Coenzyme A


Mass: 1094.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H66N7O18P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM CaCl2, 20 mM CdCl2, 20mM CoCl2, 20 mM NaCl, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.76→72.7 Å / Num. obs: 40369 / % possible obs: 100 % / Redundancy: 8 % / Net I/σ(I): 18.8
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSautoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→72.7 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1824 5 %Random selection
Rwork0.2158 ---
obs0.2176 36445 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→72.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 75 265 2569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182394
X-RAY DIFFRACTIONf_angle_d1.1483276
X-RAY DIFFRACTIONf_dihedral_angle_d15.15870
X-RAY DIFFRACTIONf_chiral_restr0.045377
X-RAY DIFFRACTIONf_plane_restr0.006413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80760.32611560.29322551X-RAY DIFFRACTION100
1.8076-1.86080.30471560.27532579X-RAY DIFFRACTION100
1.8608-1.92090.31791250.2652599X-RAY DIFFRACTION100
1.9209-1.98950.27521450.26212590X-RAY DIFFRACTION100
1.9895-2.06920.27121200.2522598X-RAY DIFFRACTION100
2.0692-2.16340.28331450.23852620X-RAY DIFFRACTION100
2.1634-2.27740.25771360.23532592X-RAY DIFFRACTION100
2.2774-2.42010.23311370.22362639X-RAY DIFFRACTION100
2.4201-2.6070.27661430.23142672X-RAY DIFFRACTION100
2.607-2.86940.30071260.22122690X-RAY DIFFRACTION100
2.8694-3.28460.2671670.21962679X-RAY DIFFRACTION100
3.2846-4.13820.21261310.18012778X-RAY DIFFRACTION100
4.1382-72.76790.21611370.18463034X-RAY DIFFRACTION99
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)
11.295-0.18131.16741.53180.32982.6921-0.0553-0.40220.14260.3115-0.0123-0.2398-0.178-0.20130.05230.22120.1166-0.00980.5174-0.03150.209716.551327.2839-8.6166
20.9463-0.13930.01160.40170.5950.9343-0.00580.0409-0.128-0.0021-0.14240.23930.0576-0.65550.10040.02960.00970.01980.6374-0.04910.25261.015316.1166-31.8694
30.11130.28460.60120.84261.76953.7347-0.0277-0.38840.15390.11910.0705-0.2764-0.17470.0815-0.05910.2630.00710.02640.3706-0.03290.26818.617229.1895-19.4162
41.9816-2.0873-0.1353.6111-0.44483.1255-0.074-0.37340.16160.25310.1759-0.45060.00360.1038-0.09460.2288-0.0104-0.04770.6237-0.05990.351426.029123.9472-7.902
51.8858-0.33970.38641.51570.61491.0285-0.014-0.2983-0.09170.24390.0111-0.11930.1909-0.1851-0.01330.17920.07590.0070.56690.01360.18113.142317.1053-13.148
65.4289-2.1673.47282.7864-1.20723.5564-0.1192-0.40380.08780.27580.1292-0.30010.1521-0.20550.0310.21690.1402-0.04280.4789-0.01860.201514.934418.4708-9.5003
74.3079-1.47791.1861.8508-0.22671.3253-0.1807-0.33930.01710.29010.1587-0.20610.0789-0.15670.02940.21230.125-0.02810.5255-0.01330.228513.881617.7512-11.9895
80.30160.5169-0.83281.8596-0.8512.9962-0.1127-0.4415-0.34960.6797-0.2510.19380.6696-0.67330.36090.8113-0.44490.1420.70370.03530.61530.7176-6.5872-22.9742
96.1342.6880.71634.5961.23312.7441-0.1967-0.0384-0.4574-0.07020.1203-0.14930.442-0.2320.06010.3574-0.0559-0.00930.1195-0.0050.314816.19951.065-34.3743
102.9855-1.0195-0.59682.64581.46292.61750.0005-0.1043-0.18010.03050.0211-0.00870.1209-0.1025-0.00260.06250.0083-0.00410.08180.02460.172817.784913.2767-33.7928
112.8764-1.4658-0.49221.73360.26611.8483-0.0176-0.13780.08980.07380.0484-0.15190.02850.1459-0.02880.06170.0732-0.02110.1502-0.00470.209522.086919.0449-28.8918
123.35680.0078-0.30650.7208-0.12670.7607-0.0241-0.2326-0.09220.12550.0543-0.26830.10130.20240.01420.12470.1604-0.04910.26730.01110.254229.455411.3571-27.8575
132.10541.1614-0.15431.40120.69891.11180.0533-0.1041-0.43360.0519-0.18060.15760.5616-0.69180.090.3347-0.20520.04290.38090.02390.24996.73446.2935-26.3948
142.49660.9787-1.02571.15820.80212.74360.0487-0.373-0.22360.0213-0.15950.10740.3709-0.7510.09770.3097-0.23190.04360.47970.04130.22193.08867.7284-20.2205
151.16580.1282-0.50071.1889-0.64490.5109-0.0806-0.162-0.18470.1750.0821-0.18930.28270.12490.00280.39750.1288-0.04020.13530.03630.316223.47353.4195-28.0881
163.70010.4791-2.20671.16290.2683.6567-0.0458-0.4084-0.44820.5164-0.14660.26450.6649-0.60740.21590.7317-0.26360.10920.43310.06740.47066.2612-2.8533-21.3239
172.1259-0.3799-0.58531.74820.57092.3761-0.0706-0.2918-0.55140.4377-0.12240.24690.6336-0.61590.17620.6175-0.2340.07670.40850.09780.32787.66931.0326-19.5583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 152 )
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 169 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 10 )
9X-RAY DIFFRACTION9chain 'B' and (resid 11 through 16 )
10X-RAY DIFFRACTION10chain 'B' and (resid 17 through 27 )
11X-RAY DIFFRACTION11chain 'B' and (resid 28 through 36 )
12X-RAY DIFFRACTION12chain 'B' and (resid 37 through 51 )
13X-RAY DIFFRACTION13chain 'B' and (resid 52 through 67 )
14X-RAY DIFFRACTION14chain 'B' and (resid 68 through 80 )
15X-RAY DIFFRACTION15chain 'B' and (resid 81 through 88 )
16X-RAY DIFFRACTION16chain 'B' and (resid 89 through 100 )
17X-RAY DIFFRACTION17chain 'B' and (resid 101 through 126 )

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