[English] 日本語
Yorodumi
- PDB-4kem: Crystal structure of a tartrate dehydratase from azospirillum, ta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kem
TitleCrystal structure of a tartrate dehydratase from azospirillum, target efi-502395, with bound mg and a putative acrylate ion, ordered active site
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsLYASE / TARTRATE DEHYDRATASE / MANDELATE RACEMASE FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


D(-)-tartrate dehydratase activity / metal ion binding
Similarity search - Function
D-tartrate dehydratase / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily ...D-tartrate dehydratase / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACRYLIC ACID / Mandelate racemase/muconate lactonizing enzyme
Similarity search - Component
Biological speciesAzospirillum sp. B510 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVetting, M.W. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. ...Vetting, M.W. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a tartrate dehydratase from azospirillum, target efi-502395, with bound mg and a putative acrylate ion, ordered active site
Authors: Vetting, M.W. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_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.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: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,37112
Polymers85,9652
Non-polymers40510
Water21,9961221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-43 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.167, 82.925, 103.266
Angle α, β, γ (deg.)90.000, 100.860, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is dimer

-
Components

#1: Protein Mandelate racemase/muconate lactonizing enzyme


Mass: 42982.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum sp. B510 (bacteria) / Strain: sp. B510 / Gene: AZL_d02920 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3P639
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AKR / ACRYLIC ACID / Acrylic acid


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1221 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Protein (30 mM NaCl, 2% glycerol, 200 mM MesoTartrate); Reservoir (100 mM Hepes pH 7.6, 20 mM Mg, 20% PolyAcrylic Acid NaSalt 5100); Cryoprotection (reservoir + 20% glycerol), sitting drop ...Details: Protein (30 mM NaCl, 2% glycerol, 200 mM MesoTartrate); Reservoir (100 mM Hepes pH 7.6, 20 mM Mg, 20% PolyAcrylic Acid NaSalt 5100); Cryoprotection (reservoir + 20% glycerol), sitting drop vapor diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 6, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. all: 189451 / Num. obs: 189451 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.6
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.596 / % possible all: 56.2

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DW7

2dw7


Resolution: 1.3→21.399 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.886 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 9474 5 %RANDOM
Rwork0.1644 ---
all0.1655 189399 --
obs0.1655 189399 93.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.15 Å2 / Biso mean: 13.0523 Å2 / Biso min: 3.65 Å2
Refinement stepCycle: LAST / Resolution: 1.3→21.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6046 0 18 1221 7285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086227
X-RAY DIFFRACTIONf_angle_d1.2298443
X-RAY DIFFRACTIONf_chiral_restr0.071884
X-RAY DIFFRACTIONf_plane_restr0.0071121
X-RAY DIFFRACTIONf_dihedral_angle_d12.0882285
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 (%)
1.3-1.31480.27332910.26615630592187
1.3148-1.33020.26943010.25135593589488
1.3302-1.34650.24192690.24025708597788
1.3465-1.36350.23963400.2365637597788
1.3635-1.38140.2513100.22415666597689
1.3814-1.40040.22823000.21875777607789
1.4004-1.42040.22823100.21155675598589
1.4204-1.44160.2312720.20585798607089
1.4416-1.46410.23273330.19925816614991
1.4641-1.48810.23462880.19495821610991
1.4881-1.51370.19763260.17655877620391
1.5137-1.54120.18653150.17025860617592
1.5412-1.57090.21713250.16525928625392
1.5709-1.60290.19542970.16095968626593
1.6029-1.63780.19342980.15716020631893
1.6378-1.67590.18362970.15286043634093
1.6759-1.71780.18223220.1536002632494
1.7178-1.76420.17932830.15556113639694
1.7642-1.81610.19323240.15716063638794
1.8161-1.87460.18093440.1526069641395
1.8746-1.94160.17183190.15386199651896
1.9416-2.01930.17073210.1536187650896
2.0193-2.11110.17473350.15316209654496
2.1111-2.22230.16753370.15416187652497
2.2223-2.36140.16553290.14846320664997
2.3614-2.54340.17493290.14376287661698
2.5434-2.79890.16143480.14746305665398
2.7989-3.20270.17343320.15156345667798
3.2027-4.03070.16023240.14756386671098
4.0307-21.40180.18043550.16256436679198
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)
10.6288-0.0994-0.15961.65870.55051.19380.0161-0.02190.03960.0598-0.07140.2458-0.1256-0.19070.06550.07660.01760.00220.07980.01870.0761-6.793422.746120.3428
20.4262-0.40190.08710.758-0.26970.4268-0.0363-0.082-0.06330.10770.06610.0965-0.0495-0.0508-0.02380.0730.00380.010.07830.0190.0761-2.578219.639626.1571
30.4863-0.1660.1910.3456-0.52790.65-0.0761-0.08140.04340.29390.0560.0026-0.2653-0.02060.010.15380.0136-0.00110.0699-0.00130.04773.818528.885830.1402
40.12940.0538-0.08841.48930.1480.4475-0.03240.03090.0138-0.15430.00230.0207-0.07290.00010.02410.06690.0071-0.02240.05370.00480.05493.662625.70782.8017
50.2387-0.04790.09850.50920.07280.65980.0030.0538-0.0089-0.1047-0.0021-0.01860.00450.0794-0.00050.0683-0.00070.00170.05830.00570.039415.170813.45853.9248
60.5506-0.21760.12610.6152-0.18980.4617-0.00850.01220.0166-0.01160.01120.0379-0.0295-0.02220.00070.081-0.0029-0.00610.05830.0040.05233.272428.701511.4365
70.6422-0.02010.28490.9820.07370.86690.033-0.0491-0.1149-0.03210.03160.19790.0824-0.1436-0.01210.0631-0.0129-0.01130.06930.03090.0978-1.35250.464634.674
80.4185-0.1821-0.00870.2835-0.28310.54570.05040.0494-0.094-0.23760.06720.20280.2351-0.0669-0.06840.1476-0.025-0.05970.06930.01080.09242.0723-6.953223.5222
90.17910.15030.11141.17290.09380.16540.0003-0.0334-0.01660.08330.0101-0.05080.04170.0017-0.010.09390.00470.00120.06050.00170.03919.50961.251448.3699
100.50470.13760.10170.9209-0.24651.3603-0.01450.02940.01660.0442-0.0106-0.0852-0.00740.08350.03480.04310.0004-0.00240.0580.00250.053528.352812.208139.1988
110.59020.0625-0.11360.7693-0.27320.5466-0.00880.0098-0.0136-0.05270.0092-0.03120.0590.0401-0.00690.06320.0056-0.00450.0503-0.00050.040419.7565-0.401732.8654
120.70670.10940.44221.1491-0.28771.15360.0287-0.02280.0530.12970.0370.1740.031-0.1264-0.05080.0843-0.00680.01830.07040.02250.08084.7512-9.876145.8945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 45 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 71 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 126 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 174 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 296 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 297 through 390 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 71 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 72 through 126 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 203 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 204 through 254 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 255 through 351 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 352 through 390 )B0

+
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