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- PDB-1gtt: CRYSTAL STRUCTURE OF HPCE -

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Basic information

Entry
Database: PDB / ID: 1gtt
TitleCRYSTAL STRUCTURE OF HPCE
Components4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
KeywordsISOMERASE / LYASE / BIFUNCTIONAL ENZYME / MULTIFUNCTIONAL ENZYME DECARBOXYLASE / AROMATIC HYDROCARBONS CATABOLISM
Function / homology
Function and homology information


5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase / 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase activity / 5-carboxymethyl-2-hydroxymuconate Delta-isomerase / 4-hydroxyphenylacetate catabolic process / 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity / metal ion binding
Similarity search - Function
4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit / 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit / 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
Homoprotocatechuate catabolism bifunctional isomerase/decarboxylase / 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.7 Å
AuthorsTame, J.R.H. / Namba, K. / Dodson, E.J. / Roper, D.I.
CitationJournal: Biochemistry / Year: 2002
Title: The Crystal Structure of Hpce, a Bifunctional Decarboxylase/Isomerase with a Multifunctional Fold.
Authors: Tame, J.R.H. / Namba, K. / Dodson, E.J. / Roper, D.I.
History
DepositionJan 18, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
B: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
C: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
D: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,7778
Polymers188,6174
Non-polymers1604
Water21,9241217
1
A: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1942
Polymers47,1541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1942
Polymers47,1541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1942
Polymers47,1541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1942
Polymers47,1541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.084, 138.201, 103.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE


Mass: 47154.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q46978, UniProt: P37352*PLUS, 5-carboxymethyl-2-hydroxymuconate Delta-isomerase, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 50.3 %
Crystal growpH: 8
Details: MONOMETHYLETHER PEG2000, CALCIUM CHLORIDE, TRIS, pH 8.00

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. obs: 196319 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.6
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.1.06refinement
MARdata reduction
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.7→91.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.134 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 9927 5.1 %RANDOM
Rwork0.216 ---
obs0.217 186453 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.7→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13007 0 4 1217 14228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02213198
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211978
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.0021.96517965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.595152072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0751585
X-RAY DIFFRACTIONr_chiral_restr0.1210.22037
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214752
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022517
X-RAY DIFFRACTIONr_nbd_refined0.2190.22343
X-RAY DIFFRACTIONr_nbd_other0.2720.213597
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.27426
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2965
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.2121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2441.58376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06213538
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.00834821
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7214.54427
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 707
Rwork0.296 13120

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