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- PDB-4ifr: 2.40 Angstroms X-ray crystal structure of R239A 2-amino-3-carboxy... -

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Basic information

Entry
Database: PDB / ID: 4ifr
Title2.40 Angstroms X-ray crystal structure of R239A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens
Components2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
KeywordsLYASE / TIM-BARREL / Decarboxylase / Metal-binding
Function / homology
Function and homology information


aminocarboxymuconate-semialdehyde decarboxylase / secondary metabolic process / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol
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: 2.391 Å
AuthorsHuo, L. / Davis, I. / Chen, L. / Liu, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The power of two: arginine 51 and arginine 239* from a neighboring subunit are essential for catalysis in alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase.
Authors: Huo, L. / Davis, I. / Chen, L. / Liu, A.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 20, 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_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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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

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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)73,3484
Polymers73,2182
Non-polymers1312
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-115 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.162, 91.162, 167.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 36608.797 Da / Num. of mol.: 2 / Mutation: R239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: KU-7 / Gene: nbaD / Plasmid: PET16b / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 0.1 M Tris pH 8.75, 0.2 M MgCl2, 17% PEG5000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.391→35 Å / Num. all: 28794 / Num. obs: 28679 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Rmerge(I) obs: 0.099 / Χ2: 2.021 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.447.50.79313430.734195.7
2.44-2.4910.20.76413960.727199.1
2.49-2.5313.10.71514120.771100
2.53-2.5915.60.6213890.872199.9
2.59-2.6417.60.50514230.9361100
2.64-2.719.60.5114271.067199.9
2.7-2.7721.80.45114031.0281100
2.77-2.8523.80.41214041.061199.9
2.85-2.93250.32314181.1911100
2.93-3.0225.90.27714101.2691100
3.02-3.13260.21914301.4291100
3.13-3.26260.17914411.7741100
3.26-3.425.90.13914352.2341100
3.4-3.5825.70.12114222.7331100
3.58-3.8125.80.10414543.0011100
3.81-4.126.10.09614433.222199.9
4.1-4.5126.40.09414613.2821100
4.51-5.1725.90.08714743.414199.8
5.17-6.526.30.07914993.097199.7
6.5-3523.20.07415952.521198.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HBV

2hbv


Resolution: 2.391→31.525 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7235 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 32.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1452 5.07 %RANDOM
Rwork0.2098 ---
all0.2139 28789 --
obs0.2139 28613 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.611 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 143.9 Å2 / Biso mean: 78.1382 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.4355 Å20 Å2-0 Å2
2--1.4355 Å2-0 Å2
3----2.871 Å2
Refinement stepCycle: LAST / Resolution: 2.391→31.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 2 26 5172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095287
X-RAY DIFFRACTIONf_angle_d1.2367166
X-RAY DIFFRACTIONf_chiral_restr0.088761
X-RAY DIFFRACTIONf_plane_restr0.006944
X-RAY DIFFRACTIONf_dihedral_angle_d16.1911923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.391-2.47650.39661200.34452570269095
2.4765-2.57560.39991400.304526612801100
2.5756-2.69270.36971420.29327032845100
2.6927-2.83460.36291370.290126722809100
2.8346-3.01210.37821390.278526932832100
3.0121-3.24440.30871590.268927132872100
3.2444-3.57050.3331680.235126862854100
3.5705-4.08620.2831600.206827322892100
4.0862-5.14460.27761470.175727942941100
5.1446-31.52770.24611400.17022937307799

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