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- PDB-4ifo: 2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxym... -

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Basic information

Entry
Database: PDB / ID: 4ifo
Title2.50 Angstroms X-ray crystal structure of R51A 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pseudomonas fluorescens
Components2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
KeywordsLYASE / TIM BARREL / Decarboxylation / Metal-binding
Function / homology
Function and homology information


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: 2.5 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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)73,6074
Polymers73,4762
Non-polymers1312
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-111 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.210, 91.210, 170.466
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: 36737.977 Da / Num. of mol.: 2 / Mutation: R51A
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.: 100 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
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: Apr 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. all: 25687 / Num. obs: 25661 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Rmerge(I) obs: 0.078 / Χ2: 0.908 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5411.40.6412500.451100
2.54-2.5912.60.58112590.4751100
2.59-2.6413.50.49912560.4571100
2.64-2.6913.90.43512660.4811100
2.69-2.7514.50.41112560.4861100
2.75-2.8214.60.35712460.4751100
2.82-2.8914.80.28612690.4841100
2.89-2.9614.90.24212730.5051100
2.96-3.0515.10.2112550.5251100
3.05-3.1515.30.16812690.5241100
3.15-3.2615.70.12812580.5831100
3.26-3.3915.80.10313060.671100
3.39-3.5516.10.08512370.7621100
3.55-3.7316.20.07112950.8631100
3.73-3.9716.60.06513071.034199.9
3.97-4.2717.10.0612781.2771100
4.27-4.7180.0612991.703199.9
4.7-5.3819.60.06213351.802199.9
5.38-6.7720.80.05313261.3811100
6.77-3519.30.04214211.723197.6

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Processing

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

2hbv


Resolution: 2.5→23.313 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8013 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1304 5.09 %RANDOM
Rwork0.197 ---
all0.1994 25634 --
obs0.1994 25616 99.93 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.35 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 105.71 Å2 / Biso mean: 54.0996 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--2.8471 Å2-0 Å2-0 Å2
2---2.8471 Å20 Å2
3---5.6942 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 2 100 5264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015287
X-RAY DIFFRACTIONf_angle_d1.1757166
X-RAY DIFFRACTIONf_chiral_restr0.083761
X-RAY DIFFRACTIONf_plane_restr0.005944
X-RAY DIFFRACTIONf_dihedral_angle_d15.2341923
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5003-2.60020.31221370.27762644278199
2.6002-2.71840.34841360.254926382774100
2.7184-2.86150.29821390.25226662805100
2.8615-3.04040.28481430.237226732816100
3.0404-3.27460.32171480.232926552803100
3.2746-3.6030.2491460.22226792825100
3.603-4.12190.24681560.181527032859100
4.1219-5.18370.20351480.162627382886100
5.1837-23.31430.19091510.161129163067100

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