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- PDB-4ih3: 2.5 Angstroms X-ray crystal structure of of human 2-amino-3-carbo... -

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Basic information

Entry
Database: PDB / ID: 4ih3
Title2.5 Angstroms X-ray crystal structure of of human 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase in complex with dipicolinic acid
Components2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
KeywordsLYASE / TIM-Barrel / Decarboxylation / Metal-binding
Function / homology
Function and homology information


aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from L-tryptophan / aminocarboxymuconate-semialdehyde decarboxylase / secondary metabolic process / L-tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding ...aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from L-tryptophan / aminocarboxymuconate-semialdehyde decarboxylase / secondary metabolic process / L-tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding / cytoplasm / 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
PYRIDINE-2,6-DICARBOXYLIC ACID / 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.493 Å
AuthorsHuo, L. / Liu, A.
CitationJournal: Proteins / Year: 2015
Title: Human alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD): A structural and mechanistic unveiling.
Authors: Huo, L. / Liu, F. / Iwaki, H. / Li, T. / Hasegawa, Y. / Liu, A.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Sep 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_label_asym_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
C: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
D: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
E: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
F: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,69918
Polymers225,3046
Non-polymers1,39512
Water5,152286
1
A: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
F: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5666
Polymers75,1012
Non-polymers4654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-107 kcal/mol
Surface area25290 Å2
MethodPISA
2
B: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
C: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5666
Polymers75,1012
Non-polymers4654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-109 kcal/mol
Surface area25080 Å2
MethodPISA
3
D: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
E: 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5666
Polymers75,1012
Non-polymers4654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-104 kcal/mol
Surface area25260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.368, 100.655, 233.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37550.629 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACMSD / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TDX5, aminocarboxymuconate-semialdehyde decarboxylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PDC / PYRIDINE-2,6-DICARBOXYLIC ACID / DIPICOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Lithium Sulfate Monohydrate, 0.1 M Bis-Tris, 25% PEG3350, pH 6.5, 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: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.493→45 Å / Num. all: 73312 / Num. obs: 55277 / % possible obs: 75.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.099 / Χ2: 1.667 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.548.50.29324730.804167.7
2.54-2.598.80.28824870.832169.2
2.59-2.649.20.27925480.851170.8
2.64-2.699.40.28925970.973171
2.69-2.759.80.25825980.916172.5
2.75-2.82100.22926270.958172.7
2.82-2.8910.10.21326690.987173.6
2.89-2.9610.30.18627011.044173.7
2.96-3.0510.30.18226501.057173.1
3.05-3.1510.40.15126621.108173.7
3.15-3.2610.30.12626681.3173.2
3.26-3.3910.30.10626371.512172.4
3.39-3.5510.10.126441.696172.3
3.55-3.7310.10.09326721.976172.4
3.73-3.979.90.08326362.299172.5
3.97-4.279.40.07327652.428175.1
4.27-4.78.90.06228692.486177.5
4.7-5.388.80.05930172.48181
5.38-6.789.30.06634532.483191.7
6.78-4510.20.06339043.622198.7

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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 2WM1

2wm1


Resolution: 2.493→35.209 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.757 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2828 2809 5.09 %Random
Rwork0.1976 ---
all0.202 73394 --
obs0.202 55192 75.2 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.772 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 99.95 Å2 / Biso mean: 33.2594 Å2 / Biso min: 11.29 Å2
Baniso -1Baniso -2Baniso -3
1-5.4051 Å20 Å2-0 Å2
2--3.1542 Å2-0 Å2
3----8.5593 Å2
Refinement stepCycle: LAST / Resolution: 2.493→35.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15810 0 78 286 16174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02916336
X-RAY DIFFRACTIONf_angle_d1.26222120
X-RAY DIFFRACTIONf_chiral_restr0.0752352
X-RAY DIFFRACTIONf_plane_restr0.0052832
X-RAY DIFFRACTIONf_dihedral_angle_d15.876114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4925-2.53550.33971150.20522160227563
2.5355-2.58160.36011120.22212402251469
2.5816-2.63120.35131420.23232416255871
2.6312-2.68490.36461350.22572430256571
2.6849-2.74320.33251240.2242508263273
2.7432-2.8070.32891350.22772511264673
2.807-2.87720.3421390.2312527266674
2.8772-2.9550.39861540.2282538269274
2.955-3.04190.34451330.23192528266173
3.0419-3.140.36991290.22652553268274
3.14-3.25210.29581300.21792539266973
3.2521-3.38220.29171470.20962493264072
3.3822-3.5360.30521500.20312514266473
3.536-3.72230.26591180.18312535265372
3.7223-3.95520.26621260.17672531265773
3.9552-4.26010.22941340.16052632276675
4.2601-4.68790.23481260.14812741286778
4.6879-5.36420.23161780.17692856303481
5.3642-6.75060.30561560.2163299345592
6.7506-35.21260.21722260.19543670389699

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