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- PDB-2eb4: Crystal structure of apo-HpcG -

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Basic information

Entry
Database: PDB / ID: 2eb4
TitleCrystal structure of apo-HpcG
Components2-oxo-hept-3-ene-1,7-dioate hydratase
KeywordsLYASE / hydratase
Function / homology
Function and homology information


2-hydroxyhexa-2,4-dienoate hydratase / 2-oxo-hept-3-ene-1,7-dioate hydratase activity / 2-hydroxyhexa-2,4-dienoate hydratase activity / 2-oxo-3-hexenedioate decarboxylase / 4-oxalocrotonate decarboxylase activity / 2-oxopent-4-enoate hydratase / 2-oxopent-4-enoate hydratase activity / : / metal ion binding
Similarity search - Function
2-oxo-hepta-4-ene-1,7-dioic acid hydratase / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / 2-hydroxyhexa-2,4-dienoate hydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsIzumi, A. / Rea, D. / Adachi, T. / Unzai, S. / Park, S.Y. / Roper, D.I. / Tame, J.R.H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Mechanism of HpcG, a Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia coli
Authors: Izumi, A. / Rea, D. / Adachi, T. / Unzai, S. / Park, S.Y. / Roper, D.I. / Tame, J.R.H.
History
DepositionFeb 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2007Provider: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-oxo-hept-3-ene-1,7-dioate hydratase
B: 2-oxo-hept-3-ene-1,7-dioate hydratase
C: 2-oxo-hept-3-ene-1,7-dioate hydratase
D: 2-oxo-hept-3-ene-1,7-dioate hydratase
E: 2-oxo-hept-3-ene-1,7-dioate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,39219
Polymers148,7545
Non-polymers63814
Water18,1591008
1
A: 2-oxo-hept-3-ene-1,7-dioate hydratase
B: 2-oxo-hept-3-ene-1,7-dioate hydratase
C: 2-oxo-hept-3-ene-1,7-dioate hydratase
D: 2-oxo-hept-3-ene-1,7-dioate hydratase
E: 2-oxo-hept-3-ene-1,7-dioate hydratase
hetero molecules

A: 2-oxo-hept-3-ene-1,7-dioate hydratase
B: 2-oxo-hept-3-ene-1,7-dioate hydratase
C: 2-oxo-hept-3-ene-1,7-dioate hydratase
D: 2-oxo-hept-3-ene-1,7-dioate hydratase
E: 2-oxo-hept-3-ene-1,7-dioate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,78438
Polymers297,50810
Non-polymers1,27528
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)136.740, 136.740, 192.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22C
13D
23C
14E
24C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 1 - 60 / Label seq-ID: 1 - 60

Dom-IDEns-IDRefine codeAuth asym-IDLabel asym-ID
112AA
212CC
123BB
223CC
133DD
233CC
142EE
242CC

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
2-oxo-hept-3-ene-1,7-dioate hydratase / 2-oxo-hept-4-ene-1 / 7-dioate hydratase


Mass: 29750.828 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: strain C / Gene: hpcG / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q46982, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1008 / 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: 3.03 Å3/Da / Density % sol: 59.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 7% PEG 12000, 0.1M MES, 0.7M potassium thiocyanate, 7% PEG 550 MME, 10mM DTT, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 14, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 223282 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.406 / % possible all: 68.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.827 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 11170 5 %RANDOM
Rwork0.20611 ---
obs0.20725 211972 93.34 %-
all-223282 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10248 0 32 1008 11288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210481
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9614206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31951299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.11423.671493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.223151741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2791586
X-RAY DIFFRACTIONr_chiral_restr0.0760.21584
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028016
X-RAY DIFFRACTIONr_nbd_refined0.2120.25062
X-RAY DIFFRACTIONr_nbtor_refined0.3020.27176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2938
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.2235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.277
X-RAY DIFFRACTIONr_mcbond_it0.4831.56533
X-RAY DIFFRACTIONr_mcangle_it0.931210508
X-RAY DIFFRACTIONr_scbond_it1.33533948
X-RAY DIFFRACTIONr_scangle_it2.2834.53698
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A240tight positional0.030.05
2B240tight positional0.030.05
3D240tight positional0.020.05
4E240tight positional0.030.05
1A261medium positional0.480.5
4E261medium positional0.630.5
2B261loose positional0.495
3D261loose positional0.595
1A240tight thermal0.130.5
2B240tight thermal0.080.5
3D240tight thermal0.30.5
4E240tight thermal0.110.5
1A261medium thermal0.692
4E261medium thermal0.572
2B261loose thermal0.6610
3D261loose thermal1.7110
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 530 -
Rwork0.304 10362 -
obs--62.57 %

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