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- PDB-4eri: Evidence for a Dual Role of an Active Site Histidine in alpha-Ami... -

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Basic information

Entry
Database: PDB / ID: 4eri
TitleEvidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase
Components2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
KeywordsLYASE / TIM Barrel / Decarboxylase / metal-binding / Zn
Function / homology
Function and homology information


organic substance metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0006 Å
AuthorsHuo, L. / Fielding, A.J. / Chen, Y. / Li, T. / Iwaki, H. / Hosler, J.P. / Chen, L. / Hasegawa, Y. / Que Jr., L. / Liu, A.
CitationJournal: Biochemistry / Year: 2012
Title: Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase
Authors: Huo, L. / Fielding, A.J. / Chen, Y. / Li, T. / Iwaki, H. / Hosler, J.P. / Chen, L. / Hasegawa, Y. / Que, L. / Liu, A.
History
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: 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 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
B: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5725
Polymers74,4172
Non-polymers1553
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-34 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.836, 48.561, 110.201
Angle α, β, γ (deg.)90.00, 126.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

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Components

#1: Protein 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase


Mass: 37208.621 Da / Num. of mol.: 2 / Mutation: H228Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: KU-7 / Gene: nbaD / Plasmid: pET16Bb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83V25
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 0.2 M MgCl2, 0.1 M Tris, 15% PEG 5000, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 44304 / Num. obs: 41070 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 51.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 6.02 / Num. unique all: 1195 / % possible all: 54.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HBV

2hbv


Resolution: 2.0006→30.757 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 2073 5.05 %RANDOM
Rwork0.2045 ---
obs0.2071 41012 92.46 %-
all-44356 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.197 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.699 Å20 Å21.3361 Å2
2--12.6084 Å2-0 Å2
3----3.9094 Å2
Refinement stepCycle: LAST / Resolution: 2.0006→30.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 3 209 5381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085328
X-RAY DIFFRACTIONf_angle_d1.0987219
X-RAY DIFFRACTIONf_dihedral_angle_d15.2051952
X-RAY DIFFRACTIONf_chiral_restr0.078765
X-RAY DIFFRACTIONf_plane_restr0.005950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0006-2.04710.40351050.25921535X-RAY DIFFRACTION56
2.0471-2.09830.2593910.24672089X-RAY DIFFRACTION75
2.0983-2.1550.28851290.23942311X-RAY DIFFRACTION83
2.155-2.21840.31881300.23872454X-RAY DIFFRACTION88
2.2184-2.290.27521240.2362600X-RAY DIFFRACTION93
2.29-2.37180.28351590.22042675X-RAY DIFFRACTION97
2.3718-2.46680.32321510.23322759X-RAY DIFFRACTION99
2.4668-2.5790.29721460.23772788X-RAY DIFFRACTION100
2.579-2.71490.29851290.22252818X-RAY DIFFRACTION99
2.7149-2.88480.31191530.22552776X-RAY DIFFRACTION100
2.8848-3.10740.25271550.22642807X-RAY DIFFRACTION100
3.1074-3.41970.27541690.21222797X-RAY DIFFRACTION100
3.4197-3.91370.22071370.18712812X-RAY DIFFRACTION100
3.9137-4.92760.20041420.1692865X-RAY DIFFRACTION100
4.9276-30.76110.22931530.18432853X-RAY DIFFRACTION97

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