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- PDB-4knp: Crystal Structure Of a Putative enoyl-coA hydratase (PSI-NYSGRC-0... -

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Basic information

Entry
Database: PDB / ID: 4knp
TitleCrystal Structure Of a Putative enoyl-coA hydratase (PSI-NYSGRC-019597) from Mycobacterium avium paratuberculosis K-10
Componentsenoyl-CoA hydratase
KeywordsLYASE / Enoyl-coA / hydratase / Protein structure initiative / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
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 / 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 ...: / 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 / 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 speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 1.898 Å
AuthorsKumar, P.R. / Ahmed, M. / Attonito, J. / Bhosle, R. / Chamala, S. / Chowdhury, S. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Love, J.D. ...Kumar, P.R. / Ahmed, M. / Attonito, J. / Bhosle, R. / Chamala, S. / Chowdhury, S. / Glenn, A.S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Seidel, R. / Stead, M. / Toro, R. / Wasserman, S.R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a Putative enoyl-coA hydratase from Mycobacterium avium paratuberculosis K-10
Authors: Kumar, P.R. / Hillerich, B. / Love, J. / Seidel, R. / Almo, S.C.
History
DepositionMay 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_initial_refinement_model / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)30,1901
Polymers30,1901
Non-polymers00
Water1,33374
1
A: enoyl-CoA hydratase

A: enoyl-CoA hydratase

A: enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)90,5703
Polymers90,5703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7080 Å2
ΔGint-33 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.971, 80.971, 91.364
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein enoyl-CoA hydratase


Mass: 30189.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: K-10 / Gene: echA7, MAP_0909c / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q742C8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 1.91 Å3/Da / Density % sol: 35.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (0.2M Calcium Acetate, 40% PEG 300, 0.1M Sodium Cacodylate, pH(6.5) - MCSG1 #46); Cryoprotection (Xylitol), Vapor ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, 5mM DTT; Reservoir (0.2M Calcium Acetate, 40% PEG 300, 0.1M Sodium Cacodylate, pH(6.5) - MCSG1 #46); Cryoprotection (Xylitol), Vapor Diffusion, Sitting Drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 28, 2013 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.36
ReflectionResolution: 1.9→50 Å / Num. all: 17671 / Num. obs: 17650 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.083 / Χ2: 1.411 / Net I/σ(I): 27.93
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.936.40.9139031.0321100
1.93-1.976.40.7938780.9811100
1.97-2.016.40.6738710.9981100
2.01-2.056.40.5698801.0321100
2.05-2.096.40.478861.0751100
2.09-2.146.40.3739121.0821100
2.14-2.196.40.3338561.0851100
2.19-2.256.40.2988811.1221100
2.25-2.326.50.248971.1261100
2.32-2.396.50.1888721.1221100
2.39-2.486.50.158801.0831100
2.48-2.586.50.1358711.1331100
2.58-2.76.50.1258891.171100
2.7-2.846.50.1018951.3281100
2.84-3.026.50.0948621.6641100
3.02-3.256.30.088922.2311100
3.25-3.586.10.0668812.5431100
3.58-4.096.30.059022.4781100
4.09-5.166.50.0358791.7151100
5.16-506.30.048632.347197.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
DENZOdata reduction
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: 3OC7

3oc7


Resolution: 1.898→25.455 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8277 / σ(F): 1.96 / Phase error: 25.29 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1654 896 5.08 %RANDOM
Rwork0.1329 ---
obs0.1354 17650 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.42 Å2 / Biso mean: 35.199 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: LAST / Resolution: 1.898→25.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 0 74 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081899
X-RAY DIFFRACTIONf_angle_d1.0832578
X-RAY DIFFRACTIONf_chiral_restr0.071301
X-RAY DIFFRACTIONf_plane_restr0.005344
X-RAY DIFFRACTIONf_dihedral_angle_d13.579694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8983-2.01710.24621730.22442772294594
2.0171-2.17270.20581500.1882777292795
2.1727-2.39090.18231450.162811295695
2.3909-2.73590.17361500.14352785293595
2.7359-3.44340.15181510.12352784293595
3.4434-18.54330.14111270.10652807293495
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)
16.85915.25981.30688.98960.76832.777-0.01780.0550.31740.01240.03260.4887-0.4245-0.2959-0.01030.2690.13620.02930.23120.01830.246619.215245.841130.2408
21.4767-0.65461.12270.5442-0.03072.0047-0.0128-0.11530.4552-0.0826-0.07550.2155-0.1312-0.03680.11580.26970.06540.0480.2603-0.00340.259724.127943.868528.9815
32.66640.08810.06380.4563-0.04740.96540.0897-0.02180.2891-0.0676-0.01550.0136-0.2025-0.0143-0.06290.20910.03030.04140.14870.02020.223135.526740.188431.3275
42.68250.99780.23741.62250.16811.41120.05050.00260.1209-0.07460.0125-0.0043-0.07470.01-0.05540.19250.06730.0180.1310.00960.237233.832536.351531.1387
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 60 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 94 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 182 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 262 )A0

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