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- PDB-4ofc: 2.0 Angstroms X-ray crystal structure of human 2-amino-3-carboxym... -

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Basic information

Entry
Database: PDB / ID: 4ofc
Title2.0 Angstroms X-ray crystal structure of human 2-amino-3-carboxymuconate-6-semialdehye decarboxylase
Components2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
KeywordsOXIDOREDUCTASE / TIM-barrel / Decarboxylase
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: 1.99 Å
AuthorsHuo, L. / Liu, F. / Iwaki, H. / Chen, L. / Hasegawa, Y. / 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
DepositionJan 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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

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)228,12312
Polymers227,7316
Non-polymers3926
Water17,907994
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)76,0414
Polymers75,9102
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-115 kcal/mol
Surface area25170 Å2
MethodPISA
3
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)76,0414
Polymers75,9102
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-114 kcal/mol
Surface area25170 Å2
MethodPISA
4
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)76,0414
Polymers75,9102
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-111 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.704, 101.082, 232.820
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: 37955.109 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 994 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bis-Tris, 22% PEG 3350, 0.2 M lithium sulfate, pH 7.5, 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: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→45 Å / Num. all: 150018 / Num. obs: 131416 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.153
Reflection shellResolution: 1.99→2.03 Å / % possible all: 81.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.14data extraction
SERGUIdata collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4IH3

4ih3


Resolution: 1.99→27.106 Å / FOM work R set: 0.8235 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 6186 4.99 %Random
Rwork0.1966 ---
obs0.1988 130135 86.41 %-
all-150601 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.925 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 83.97 Å2 / Biso mean: 29.88 Å2 / Biso min: 11.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.6733 Å20 Å2-0 Å2
2--0.8304 Å2-0 Å2
3----3.5037 Å2
Refinement stepCycle: LAST / Resolution: 1.99→27.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15984 0 6 994 16984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816416
X-RAY DIFFRACTIONf_angle_d1.15522206
X-RAY DIFFRACTIONf_chiral_restr0.0772370
X-RAY DIFFRACTIONf_plane_restr0.0062844
X-RAY DIFFRACTIONf_dihedral_angle_d15.646138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9595-1.98180.3141610.25453190335167
1.9818-2.00510.26721830.23453766394979
2.0051-2.02960.28571960.22383755395180
2.0296-2.05520.29951870.22333800398780
2.0552-2.08230.28091840.21753811399581
2.0823-2.11080.28331960.22113840403681
2.1108-2.14090.29012180.2223739395780
2.1409-2.17290.27812060.21513780398680
2.1729-2.20680.26722380.21763799403781
2.2068-2.2430.29842100.21743793400380
2.243-2.28160.27391830.20973808399180
2.2816-2.32310.26651930.21293839403281
2.3231-2.36780.25582180.2153830404882
2.3678-2.41610.28992100.2143875408582
2.4161-2.46860.27142280.20883916414482
2.4686-2.52590.26342070.20963929413683
2.5259-2.58910.28381990.20924012421184
2.5891-2.6590.26421990.21523991419084
2.659-2.73720.2852190.20994071429086
2.7372-2.82540.2492300.21914123435387
2.8254-2.92630.25572480.21794271451990
2.9263-3.04330.27062290.22644388461792
3.0433-3.18160.2542650.21674535480095
3.1816-3.34910.24772390.19964623486297
3.3491-3.55850.24562380.19134725496398
3.5585-3.83260.21132210.17994787500899
3.8326-4.21690.18862580.16064797505599
4.2169-4.82420.18582330.1548365069100
4.8242-6.06670.21312530.188149085161100
6.0667-27.10840.20542480.18751015349100

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