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- PDB-1szo: Crystal Structure Analysis of the 6-Oxo Camphor Hydrolase His122A... -

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Basic information

Entry
Database: PDB / ID: 1szo
TitleCrystal Structure Analysis of the 6-Oxo Camphor Hydrolase His122Ala Mutant Bound to Its Natural Product (2S,4S)-alpha-Campholinic Acid
Components6-oxocamphor hydrolase
KeywordsHYDROLASE / Enzyme-Product Complex
Function / homology
Function and homology information


6-oxocamphor hydrolase / hydrolase activity, acting on acid carbon-carbon bonds, in ketonic substances
Similarity search - Function
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
Chem-CAX / 6-oxocamphor hydrolase
Similarity search - Component
Biological speciesRhodococcus sp. NCIMB 9784 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeonard, P.M. / Grogan, G.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structure of 6-oxo camphor hydrolase H122A mutant bound to its natural product, (2S,4S)-alpha-campholinic acid: mutant structure suggests an atypical mode of transition state binding for a crotonase homolog.
Authors: Leonard, P.M. / Grogan, G.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: The 2- Crystal Structure of 6-Oxo Camphor Hydrolase. NEW STRUCTURAL DIVERSITY IN THE CROTONASE SUPERFAMILY.
Authors: Whittingham, J.L. / Turkenburg, J.P. / Verma, C.S. / Walsh, M.A. / Grogan, G.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: The Desymmetrization of Bicyclic beta-Diketones by an Enzymatic Retro-Claisen Reaction. A NEW REACTION OF THE CROTONASE SUPERFAMILY.
Authors: Grogan, G. / Roberts, G.A. / Bougioukou, D. / Turner, N.J. / Flitsch, S.L.
#3: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2001
Title: An Asymmetric Enzyme-Catalysed Retro-Claisen Reaction for the Desymmetrisation of Cyclic beta-Diketones.
Authors: Grogan, G. / Graf, J. / Jones, A. / Parsons, S. / Turner, N.J. / Flitsch, S.L.
History
DepositionApr 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-oxocamphor hydrolase
B: 6-oxocamphor hydrolase
C: 6-oxocamphor hydrolase
D: 6-oxocamphor hydrolase
E: 6-oxocamphor hydrolase
F: 6-oxocamphor hydrolase
G: 6-oxocamphor hydrolase
H: 6-oxocamphor hydrolase
I: 6-oxocamphor hydrolase
J: 6-oxocamphor hydrolase
K: 6-oxocamphor hydrolase
L: 6-oxocamphor hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)343,74928
Polymers341,35412
Non-polymers2,39516
Water34,7511929
1
A: 6-oxocamphor hydrolase
B: 6-oxocamphor hydrolase
C: 6-oxocamphor hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9377
Polymers85,3393
Non-polymers5994
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
ΔGint-31 kcal/mol
Surface area26110 Å2
MethodPISA
2
D: 6-oxocamphor hydrolase
E: 6-oxocamphor hydrolase
F: 6-oxocamphor hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9377
Polymers85,3393
Non-polymers5994
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-33 kcal/mol
Surface area26360 Å2
MethodPISA
3
G: 6-oxocamphor hydrolase
H: 6-oxocamphor hydrolase
I: 6-oxocamphor hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9377
Polymers85,3393
Non-polymers5994
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-35 kcal/mol
Surface area26250 Å2
MethodPISA
4
J: 6-oxocamphor hydrolase
K: 6-oxocamphor hydrolase
L: 6-oxocamphor hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9377
Polymers85,3393
Non-polymers5994
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-34 kcal/mol
Surface area25970 Å2
MethodPISA
5
G: 6-oxocamphor hydrolase
H: 6-oxocamphor hydrolase
I: 6-oxocamphor hydrolase
J: 6-oxocamphor hydrolase
K: 6-oxocamphor hydrolase
L: 6-oxocamphor hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,87514
Polymers170,6776
Non-polymers1,1988
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28070 Å2
ΔGint-85 kcal/mol
Surface area41880 Å2
MethodPISA
6
A: 6-oxocamphor hydrolase
B: 6-oxocamphor hydrolase
C: 6-oxocamphor hydrolase
D: 6-oxocamphor hydrolase
E: 6-oxocamphor hydrolase
F: 6-oxocamphor hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,87514
Polymers170,6776
Non-polymers1,1988
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28000 Å2
ΔGint-83 kcal/mol
Surface area41970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.280, 132.008, 135.424
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer, of which there are four complete copies in the asymmetric unit.

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Components

#1: Protein
6-oxocamphor hydrolase


Mass: 28446.172 Da / Num. of mol.: 12 / Mutation: H122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. NCIMB 9784 (bacteria) / Gene: camK / Plasmid: pET-26b (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q93TU6
#2: Chemical
ChemComp-CAX / (2S,4S)-4-(2,2-DIHYDROXYETHYL)-2,3,3-TRIMETHYLCYCLOPENTANONE / (2S,4S)-ALPHA-CAMPHOLINIC ACID


Mass: 186.248 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H18O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1929 / 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: 2.2 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG MME 2000, calcium acetate, MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2003 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 229538 / Num. obs: 229538 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.047 / Net I/σ(I): 29.2
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.9 / Num. unique all: 19032 / Rsym value: 0.241 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1O8U

1o8u


Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 11502 -Random
Rwork0.164 ---
all0.165 218036 --
obs0.164 218036 100 %-
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å2-0.3 Å2
2--0.66 Å20 Å2
3---0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.13 Å0.147 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23195 0 160 1929 25284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.663
X-RAY DIFFRACTIONr_bond_refined_d0.018
LS refinement shellResolution: 1.9→1.947 Å
RfactorNum. reflection
Rfree0.258 828
Rwork0.201 -
obs-15878

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