[English] 日本語
Yorodumi
- PDB-4igm: 2.39 Angstrom X-ray Crystal structure of human ACMSD -

+
Open data


ID or keywords:

Loading...

-
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 / aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from tryptophan / secondary metabolic process / tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding ...aminocarboxymuconate-semialdehyde decarboxylase / aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from tryptophan / secondary metabolic process / tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more