[English] 日本語
Yorodumi
- PDB-3eis: Crystal Structure of Arylmalonate Decarboxylase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eis
TitleCrystal Structure of Arylmalonate Decarboxylase
ComponentsArylmalonate decarboxylase
KeywordsLYASE / ENANTIOSELECTIVE DECARBOXYLATION / DECARBOXYLASE
Function / homology
Function and homology information


arylmalonate decarboxylase / arylmalonate decarboxylase activity
Similarity search - Function
Maleate isomerase/Arylmalonate decarboxylase / Arylmalonate decarboxylase / Rossmann fold - #12500 / Ribulose-phosphate binding barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arylmalonate decarboxylase
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsNakasako, M. / Obata, R. / Miyamoto, K. / Ohta, H.
CitationJournal: To be Published
Title: Structural Basis of the Enantioselective Decarboxylation by Arylmalonate Decarboxylase
Authors: Nakasako, M. / Obata, R. / Miyamoto, K. / Ohta, H.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arylmalonate decarboxylase
B: Arylmalonate decarboxylase
C: Arylmalonate decarboxylase
D: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,47913
Polymers99,6304
Non-polymers8499
Water7,314406
1
A: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1884
Polymers24,9081
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0963
Polymers24,9081
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1003
Polymers24,9081
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0963
Polymers24,9081
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: Arylmalonate decarboxylase
hetero molecules

C: Arylmalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1956
Polymers49,8152
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y+1/2,-z+3/21
Buried area2310 Å2
ΔGint-41 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.508, 99.395, 139.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Arylmalonate decarboxylase / / AMDase


Mass: 24907.592 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: KU1201 / Plasmid: PAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA-MCR / References: UniProt: Q05115, arylmalonate decarboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5M AMMONIUM SULFATE, 12% (W/V) GLYCEROL, 0.1M TRIS-HCL, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 68612 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 30.1 / Num. measured all: 493346
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.639 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.186 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3453 5 %RANDOM
Rwork0.195 ---
obs0.197 65102 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.629 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2---1.12 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6757 0 49 406 7212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226903
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9752.0069389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56421.933238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.884151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5481568
X-RAY DIFFRACTIONr_chiral_restr0.1720.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025148
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.33330
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.54778
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.5686
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.3137
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.560
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.73424721
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.65437335
X-RAY DIFFRACTIONr_scbond_it2.14222426
X-RAY DIFFRACTIONr_scangle_it3.12732054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 222 -
Rwork0.207 4741 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.17670.76640.34792.08191.35151.96910.04260.03540.14180.01580.0960.2341-0.07020.0794-0.1387-0.025-0.0317-0.0611-0.11090.0242-0.02924.23055.651283.8727
21.17980.6268-0.05031.0128-0.18740.6831-0.10010.0632-0.1053-0.23960.10830.05120.1787-0.0328-0.00820.0284-0.0370.0296-0.07740.0465-0.044434.841442.146383.0535
30.5378-0.0827-0.02821.3515-0.59980.7628-0.16710.14050.06810.09240.20610.054-0.0066-0.1303-0.039-0.045-0.03220.00550.01460.0225-0.094136.323826.1917116.819
40.78970.07490.14061.79111.05721.6638-0.0894-0.10620.11820.06120.1512-0.42940.1480.0955-0.0617-0.08910.01220.005-0.0571-0.0710.028424.561130.7548156.2553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 240
2X-RAY DIFFRACTION2B5 - 238
3X-RAY DIFFRACTION3C7 - 240
4X-RAY DIFFRACTION4D5 - 240

+
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