[English] 日本語
Yorodumi
- PDB-4h19: Crystal structure of an enolase (mandelate racemase subgroup, tar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h19
TitleCrystal structure of an enolase (mandelate racemase subgroup, target EFI-502087) from agrobacterium tumefaciens, with bound Mg and d-ribonohydroxamate, ordered loop
ComponentsMandelate racemase
KeywordsLYASE / Enolase / mandelate racemase subgroup / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
: / 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 ...: / 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
Chem-0YR / Mandelate racemase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVetting, M.W. / Bouvier, J.T. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / 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, target EFI-502087) from agrobacterium tumefaciens, with bound Mg and d-ribonohydroxamate, ordered loop
Authors: Vetting, M.W. / Bouvier, J.T. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_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
B: Mandelate racemase
C: Mandelate racemase
D: Mandelate racemase
E: Mandelate racemase
F: Mandelate racemase
G: Mandelate racemase
H: Mandelate racemase
I: Mandelate racemase
K: Mandelate racemase
L: Mandelate racemase
M: Mandelate racemase
N: Mandelate racemase
P: Mandelate racemase
J: Mandelate racemase
O: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)667,452151
Polymers657,97516
Non-polymers9,477135
Water104,3615793
1
A: Mandelate racemase
D: Mandelate racemase
F: Mandelate racemase
K: Mandelate racemase
hetero molecules

A: Mandelate racemase
D: Mandelate racemase
F: Mandelate racemase
K: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,25984
Polymers328,9888
Non-polymers5,27176
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_553-x,y,-z-3/21
Buried area42420 Å2
ΔGint-120 kcal/mol
Surface area79520 Å2
MethodPISA
2
B: Mandelate racemase
C: Mandelate racemase
E: Mandelate racemase
G: Mandelate racemase
H: Mandelate racemase
I: Mandelate racemase
L: Mandelate racemase
M: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,39271
Polymers328,9888
Non-polymers4,40563
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40390 Å2
ΔGint-98 kcal/mol
Surface area79670 Å2
MethodPISA
3
N: Mandelate racemase
P: Mandelate racemase
J: Mandelate racemase
O: Mandelate racemase
hetero molecules

N: Mandelate racemase
P: Mandelate racemase
J: Mandelate racemase
O: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,86276
Polymers328,9888
Non-polymers4,87468
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_653-x+1,y,-z-3/21
Buried area42110 Å2
ΔGint-147 kcal/mol
Surface area79120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.363, 395.688, 177.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-401-

CA

21D-406-

CL

31K-768-

HOH

41J-533-

HOH

51O-708-

HOH

-
Components

-
Protein , 1 types, 16 molecules ABCDEFGHIKLMNPJO

#1: Protein
Mandelate racemase


Mass: 41123.445 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: Atu4120 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7CU39

-
Non-polymers , 6 types, 5928 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-0YR / (2R,3R,4R)-N,2,3,4,5-pentakis(oxidanyl)pentanamide / D-ribonohydroxamate


Mass: 181.144 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C5H11NO6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5793 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 4
Details: Protein (10 mM Tris, pH 8.0, 200 mM NaCl, 5 mM Mg, 10 mM D-ribonohydroxamate; Reservoir (20% (w/v) PEG-8000, 100 mM Tris pH 8.5, 200 mM MgCl2); Cryoprotection (Reservoir, + 20% glycerol, 50 ...Details: Protein (10 mM Tris, pH 8.0, 200 mM NaCl, 5 mM Mg, 10 mM D-ribonohydroxamate; Reservoir (20% (w/v) PEG-8000, 100 mM Tris pH 8.5, 200 mM MgCl2); Cryoprotection (Reservoir, + 20% glycerol, 50 mM MgCl, 10 mM D-ribonohydroxamate), 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: Jul 11, 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: 1.8→197.844 Å / Num. all: 573535 / Num. obs: 573535 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.133 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.95.80.6491.2483636832990.64999.9
1.9-2.016.10.441.7478239789030.44100
2.01-2.156.30.3052.5470246741940.305100
2.15-2.326.60.2183.4458340690870.218100
2.32-2.5570.1674.4443513637330.167100
2.55-2.857.30.1335.4420273576780.133100
2.85-3.297.50.1026.5382863510140.102100
3.29-4.027.50.087.3325074432160.08100
4.02-5.697.50.0697.5251448336230.069100
5.69-197.8447.20.0666.2135941187880.06699.5

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TJ4

3tj4


Resolution: 1.8→197.84 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.47 / SU B: 2.173 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 28777 5 %RANDOM
Rwork0.1371 ---
all0.139 573175 --
obs0.139 573175 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.84 Å2 / Biso mean: 17.366 Å2 / Biso min: 6.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å20 Å2
2--0.21 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→197.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46512 0 531 5793 52836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01948400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0245288
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.94666077
X-RAY DIFFRACTIONr_angle_other_deg0.9313.001104152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48155988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30522.8692067
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.367157361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.88715321
X-RAY DIFFRACTIONr_chiral_restr0.1230.27446
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02154285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211176
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 2068 -
Rwork0.229 40074 -
all-42142 -
obs--99.82 %

+
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