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- PDB-4igm: 2.39 Angstrom X-ray Crystal structure of human ACMSD -

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Basic information

Entry
Database: PDB / ID: 4igm
Title2.39 Angstrom X-ray Crystal structure of human ACMSD
Components2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
KeywordsLYASE / TIM barrel / neurological disorder / zinc-dependent decarboxylase / kynurenine pathway
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
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.391 Å
AuthorsLiu, F. / Liu, A.
CitationJournal: To be Published
Title: 2.39 Angstrom X-ray Crystal structure of human ACMSD
Authors: Liu, F. / Liu, A.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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)225,69612
Polymers225,3046
Non-polymers3926
Water8,611478
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)75,2324
Polymers75,1012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-113 kcal/mol
Surface area25870 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)75,2324
Polymers75,1012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-114 kcal/mol
Surface area25280 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)75,2324
Polymers75,1012
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-107 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.112, 101.878, 233.455
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, human / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris 7.0, 20% PEG 3350, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.391→45 Å / Num. all: 84793 / Num. obs: 80491 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.391→2.44 Å / % possible all: 87.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.391→45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.402 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.619 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 4033 5 %RANDOM
Rwork0.2081 ---
all0.2122 84870 --
obs0.2122 80491 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.96 Å2 / Biso mean: 28.0871 Å2 / Biso min: 8.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.391→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15810 0 6 478 16294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216236
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.96921972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63651986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.46324.138696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.537152862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3881578
X-RAY DIFFRACTIONr_chiral_restr0.1160.22352
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112228
LS refinement shellResolution: 2.391→2.453 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 225 -
Rwork0.243 5038 -
all-5263 -
obs-7127 89.19 %

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