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- PDB-3hp0: Crystal structure of a Putative polyketide biosynthesis enoyl-CoA... -

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Basic information

Entry
Database: PDB / ID: 3hp0
TitleCrystal structure of a Putative polyketide biosynthesis enoyl-CoA hydratase (pksH) from Bacillus subtilis
ComponentsPutative polyketide biosynthesis enoyl-CoA hydratase homolog pksH
KeywordsLYASE / polyketide synthase / enoyl CoA hydratase / isomerase / Antibiotic biosynthesis / 11251f / PSI2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / antibiotic biosynthetic process / lyase activity / cytoplasm
Similarity search - Function
: / 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 / Alpha Beta
Similarity search - Domain/homology
Probable polyketide biosynthesis enoyl-CoA hydratase PksH
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsSatyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a Putative polyketide biosynthesis enoyl-CoA hydratase (pksH) from Bacillus subtilis
Authors: Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH
B: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH
C: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH
D: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH
E: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH
F: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)184,8306
Polymers184,8306
Non-polymers00
Water3,765209
1
A: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)30,8051
Polymers30,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)30,8051
Polymers30,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)30,8051
Polymers30,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)30,8051
Polymers30,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)30,8051
Polymers30,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)30,8051
Polymers30,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
C: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH

A: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH
E: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)92,4153
Polymers92,4153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_445x-1,y-1,z1
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-43 kcal/mol
Surface area30160 Å2
MethodPISA
8
B: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH

D: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH
F: Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Theoretical massNumber of molelcules
Total (without water)92,4153
Polymers92,4153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_665x+1,y+1,z1
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-45 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.908, 80.908, 218.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Putative polyketide biosynthesis enoyl-CoA hydratase homolog pksH


Mass: 30804.918 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: TOP10(Invitrogen) / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU17160, pksH / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: P40805, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350 200mM Ammonium(tri-) Citrate (pH 7), VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 67711 / Num. obs: 67711 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 9.5
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 6.5 / Num. unique all: 6229 / Rsym value: 0.065 / % possible all: 90.2

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.32→43.09 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: phi-psi violation is due to disorder and high B factor.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 5004 -RANDOM
Rwork0.232 ---
all0.259 66562 --
obs0.232 66562 96.4 %-
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å21.2 Å20 Å2
2---3.07 Å20 Å2
3---6.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.32→43.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11649 0 0 209 11858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_degree22.4
X-RAY DIFFRACTIONc_improper_degree0.81
LS refinement shellResolution: 2.32→2.47 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.362 680 -
Rwork0.325 --
obs-16445 74.1 %

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