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- PDB-1u2e: Crystal Structure of the C-C bond hydrolase MhpC -

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Basic information

Entry
Database: PDB / ID: 1u2e
TitleCrystal Structure of the C-C bond hydrolase MhpC
Components2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD
Function / homology
Function and homology information


2-hydroxy-6-oxonona-2,4-dienedioate hydrolase / 2-hydroxy-6-oxonona-2,4,7-trienedioate hydrolase activity / 3-(3-hydroxy)phenylpropionate catabolic process / 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity / 3-phenylpropionate catabolic process / hydrolase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase / Alpha/beta hydrolase family / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMontgomery, M.G. / Dunn, G. / Mohammed, F. / Robertson, T. / Garcia, J.-L. / Coker, A. / Bugg, T.D.H. / Wood, S.P.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Structure of the C-C Bond Hydrolase MhpC Provides Insights into its Catalytic Mechanism
Authors: Dunn, G. / Montgomery, M.G. / Mohammed, F. / Coker, A. / Cooper, J.B. / Robertson, T. / Garcia, J.-L. / Bugg, T.D.H. / Wood, S.P.
History
DepositionJul 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
B: 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
C: 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
D: 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5648
Polymers128,4234
Non-polymers1424
Water9,800544
1
A: 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
C: 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2824
Polymers64,2112
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
D: 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2824
Polymers64,2112
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.858, 144.154, 62.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase / 2-hydroxy-6-keto-nona-2 / 4-diene-1 / 9-dioic acid 5 / 6-hydrolase


Mass: 32105.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mhpC / Plasmid: pIPC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P77044, EC: 3.7.1.-
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.59 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPD, PEG 8000, Tris, Calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 73037 / Num. obs: 71688 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 6.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4674 / % possible all: 72.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAD structure of MhpC

Resolution: 2.1→20 Å / Isotropic thermal model: anisotropic / Cross valid method: Free-R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3619 -RANDOM
Rwork0.219 ---
all-71393 --
obs-71393 93.2 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8944 0 4 544 9492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.244

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