[English] 日本語
Yorodumi
- PDB-4dn1: Crystal structure of an ENOLASE (mandelate racemase subgroup memb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dn1
TitleCrystal structure of an ENOLASE (mandelate racemase subgroup member) from Agrobacterium tumefaciens (target EFI-502088) with bound mg and formate
ComponentsIsomerase/lactonizing enzyme
KeywordsISOMERASE / Enolase Family Member / Mandelate Racemase Subgroup Member / Enzyme Function Initiative / EFI / Structural Genomics
Function / homology
Function and homology information


amino acid catabolic process / isomerase activity / magnesium ion binding
Similarity search - Function
Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / 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 ...Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / 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
FORMIC ACID / Isomerase/lactonizing enzyme
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Bouvier, J.T. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Al Obaidi, N.F. / Imker, H.J. / Gerlt, J.A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Bouvier, J.T. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Al Obaidi, N.F. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: to be published
Title: Crystal structure of an enolase (mandelate racemase subgroup member) from Agrobacterium tumefaciens (target EFI-502088) with bound mg and formate
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Bouvier, J.T. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Al Obaidi, N.F. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 13, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Isomerase/lactonizing enzyme
B: Isomerase/lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1916
Polymers89,0612
Non-polymers1304
Water11,818656
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-54 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.360, 102.360, 369.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-545-

HOH

-
Components

#1: Protein Isomerase/lactonizing enzyme


Mass: 44530.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: Atu5458 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CL63
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 4.6
Details: Protein (10 mM Tris pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1 mM D,L-glycerate; Reservoir (0.1 M NaAcetate pH 4.6, 3.5 M NaFormate); Cryoprotection (Reservoir, 50 mM MgCl2, 20% Glycerol), sitting ...Details: Protein (10 mM Tris pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1 mM D,L-glycerate; Reservoir (0.1 M NaAcetate pH 4.6, 3.5 M NaFormate); Cryoprotection (Reservoir, 50 mM MgCl2, 20% Glycerol), sitting drop vapor diffuction, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 15, 2011 / 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: 2.05→50 Å / Num. obs: 72945 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 15.8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 4.5 / Num. unique all: 10419 / Rsym value: 0.517 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NQL

2nql


Resolution: 2.05→41.706 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8959 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 3677 5.04 %RANDOM
Rwork0.1614 ---
all0.1631 72945 --
obs0.1631 72945 99.98 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.172 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 175.14 Å2 / Biso mean: 29.1014 Å2 / Biso min: 9.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.7921 Å20 Å2-0 Å2
2--0.7921 Å2-0 Å2
3----1.5842 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 6 656 6640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086135
X-RAY DIFFRACTIONf_angle_d1.0538356
X-RAY DIFFRACTIONf_chiral_restr0.073907
X-RAY DIFFRACTIONf_plane_restr0.0051100
X-RAY DIFFRACTIONf_dihedral_angle_d12.2452227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.0770.3021250.246225742699
2.077-2.10540.29221330.247726342767
2.1054-2.13550.28671410.221126302771
2.1355-2.16740.27771240.201626102734
2.1674-2.20130.22521400.184625942734
2.2013-2.23730.23881600.186226152775
2.2373-2.27590.22241420.178626342776
2.2759-2.31730.25451440.171325832727
2.3173-2.36190.22331260.163126292755
2.3619-2.41010.19921330.159526242757
2.4101-2.46250.24251440.171326592803
2.4625-2.51980.17891490.166625922741
2.5198-2.58280.21941480.172426272775
2.5828-2.65260.2181310.162826582789
2.6526-2.73060.21481490.165626312780
2.7306-2.81870.19091460.169326542800
2.8187-2.91950.23641440.174526512795
2.9195-3.03630.20511240.1726712795
3.0363-3.17450.18681330.16926762809
3.1745-3.34180.16381550.16326552810
3.3418-3.5510.17391270.146927262853
3.551-3.8250.1671360.13126912827
3.825-4.20960.15841450.12327272872
4.2096-4.8180.15271620.127327342896
4.818-6.06720.15181640.147127892953
6.0672-41.71510.19341520.18230003152
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)
11.36040.13620.01890.6640.1460.5801-0.09190.0068-0.01070.00360.07020.1551-0.1151-0.18190.06530.08640.03950.0180.21360.00590.165230.113247.5176.2733
20.4495-0.1423-0.32910.5855-0.04970.5663-0.0042-0.02580.07270.03940.0757-0.0179-0.119-0.038-0.04890.06520.02680.02650.2253-0.02050.131442.33255.70549.1027
31.6482-0.4112-0.61750.7453-0.24150.4750.08350.0853-0.39180.07310.15590.33990.0623-0.23130.18520.1870.13230.0160.42390.0520.534411.778564.44985.6085
40.9651-0.29580.01780.55930.25630.23480.07860.27620.1638-0.2255-0.03090.162-0.3076-0.1815-0.01090.22310.12890.00970.30790.06080.229325.859671.1659-5.4439
50.4584-0.13480.01420.7116-00.5887-0.0105-0.01540.05840.06190.08470.086-0.1043-0.1437-0.06120.13550.05280.04320.2344-0.00610.15832.578461.958113.9898
60.8246-0.1494-0.09410.4858-0.03920.5174-0.04010.05110.0245-0.00480.0377-0.07630.00760.03270.02620.0238-0.03980.02990.2463-0.03680.149349.468141.4504-8.5848
70.79710.1427-0.19230.3425-0.07460.54120.0120.13570.0184-0.0590.0095-0.0149-0.0573-0.0406-0.01710.1049-0.01310.02010.2159-0.00490.105454.362353.1752-20.669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:38)A0 - 38
2X-RAY DIFFRACTION2chain 'A' and (resseq 39:158)A39 - 158
3X-RAY DIFFRACTION3chain 'A' and (resseq 159:193)A159 - 193
4X-RAY DIFFRACTION4chain 'A' and (resseq 194:289)A194 - 289
5X-RAY DIFFRACTION5chain 'A' and (resseq 290:388)A290 - 388
6X-RAY DIFFRACTION6chain 'B' and (resseq 1:94)B1 - 94
7X-RAY DIFFRACTION7chain 'B' and (resseq 95:388)B95 - 388

+
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