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- PDB-3g64: Crystal structure of putative enoyl-CoA hydratase from Streptomyc... -

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Basic information

Entry
Database: PDB / ID: 3g64
TitleCrystal structure of putative enoyl-CoA hydratase from Streptomyces coelicolor A3(2)
ComponentsPutative enoyl-CoA hydratase
KeywordsLYASE / alpha-beta structure / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Enoyl-CoA Hydratase from Streptomyces coelicolor A3(2)
Authors: Kim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionFeb 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Putative enoyl-CoA hydratase
B: Putative enoyl-CoA hydratase
C: Putative enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,64111
Polymers89,9793
Non-polymers6618
Water12,737707
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-94.3 kcal/mol
Surface area31630 Å2
MethodPISA
2
A: Putative enoyl-CoA hydratase
B: Putative enoyl-CoA hydratase
C: Putative enoyl-CoA hydratase
hetero molecules

A: Putative enoyl-CoA hydratase
B: Putative enoyl-CoA hydratase
C: Putative enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,28222
Polymers179,9596
Non-polymers1,32316
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area37090 Å2
ΔGint-271 kcal/mol
Surface area49710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.167, 191.297, 93.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Putative enoyl-CoA hydratase


Mass: 29993.154 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-termiinal 6-His-tag with a TEV protease cut-site
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: A3(2) / M145 / Gene: SCO5979, SCBAC16H6.14, STBAC16H6.14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93JE8

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Non-polymers , 5 types, 715 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 2.5M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2008 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.05→49.6 Å / Num. all: 123443 / Num. obs: 123443 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 27.6 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3059 / % possible all: 92.6

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Processing

Software
NameClassification
SBC-Collectdata collection
HKL-2000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→49.6 Å / SU ML: 0.22 / Isotropic thermal model: isotropic/anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
Details: All Bijvoet pairs were counted independently in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 6208 5.03 %random
Rwork0.154 ---
all0.156 123443 --
obs0.156 123443 97.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.445 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.1065 Å20 Å20 Å2
2---5.3979 Å20 Å2
3----6.7086 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6166 0 34 707 6907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.312
X-RAY DIFFRACTIONf_chiral_restr0.088
X-RAY DIFFRACTIONf_gen_planes_refined0.0006
X-RAY DIFFRACTIONf_dihedral_angle_1_deg17.19
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.05-2.07340.31491800.26473530371087
2.0734-2.09780.29591660.23913485365188
2.0978-2.12340.25931960.22923615381190
2.1234-2.15020.25391730.21883704387791
2.1502-2.17850.2171870.20243708389593
2.1785-2.20840.2522040.20493734393894
2.2084-2.23990.26621830.20813843402695
2.2399-2.27340.25692020.19363910411297
2.2734-2.30890.22282190.19223878409798
2.3089-2.34670.24722040.19133993419799
2.3467-2.38720.22582100.18113946415699
2.3872-2.43060.19172210.17323984420599
2.4306-2.47730.21312180.1613981419999
2.4773-2.52790.18951880.15983995418399
2.5279-2.58290.22262260.16043963418999
2.5829-2.6430.19951970.16583969416699
2.643-2.7090.22212310.169939794200100
2.709-2.78230.20162080.153640064214100
2.7823-2.86420.19242360.152739844220100
2.8642-2.95660.19041910.161639994190100
2.9566-3.06220.20192070.154539994206100
3.0622-3.18480.2212320.154540174249100
3.1848-3.32970.17292420.142139564198100
3.3297-3.50530.20152280.143140054233100
3.5053-3.72480.15982310.127239844215100
3.7248-4.01230.1652040.120740064210100
4.0123-4.41580.14862240.107540114235100
4.4158-5.05430.14742030.112640234226100
5.0543-6.36570.20152260.149939714197100
6.3657-49.6610.1591710.155940574228100
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)
10.1918-0.1734-0.02160.54-0.02960.47310.0017-0.0428-0.06260.08820.03990.0676-0.0566-0.1338-0.03530.09520.03250.04790.13810.02850.101245.928124.158542.5268
20.58850.0967-0.1375-0.0139-0.0420.69570.0492-0.03570.12530.10970.03260.0005-0.59210.049-0.0790.39-0.0610.04220.0791-0.04360.140463.22652.905837.5713
3-0.11870.23940.06580.61820.01660.6858-0.02520.0114-0.09580.06090.0449-0.1019-0.01880.2603-0.0288-0.0066-0.0313-0.02750.139-0.0170.09578.221423.127133.1505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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