[English] 日本語
Yorodumi
- PDB-4gfi: Crystal structure of EFI-502318, an enolase family member from Ag... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gfi
TitleCrystal structure of EFI-502318, an enolase family member from Agrobacterium tumefaciens with homology to dipeptide epimerases (bound sodium, L-Ala-L-Glu with ordered loop)
ComponentsMandelate racemase/muconate lactonizing enzyme family protein
KeywordsISOMERASE / putative L-ALA-L/D-GLU epimerase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / metal ion binding
Similarity search - Function
Dipeptide epimerase / 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 ...Dipeptide epimerase / 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
ALANINE / GLUTAMIC ACID / Dipeptide epimerase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 EFI-502318, an enolase family member from Agrobacterium tumefaciens with homology to dipeptide epimerases (bound sodium, l-ala-l-glu with 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
DepositionAug 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 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_conn_type / 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.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: Mandelate racemase/muconate lactonizing enzyme family protein
B: Mandelate racemase/muconate lactonizing enzyme family protein
C: Mandelate racemase/muconate lactonizing enzyme family protein
D: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,91926
Polymers141,2294
Non-polymers1,69022
Water12,629701
1
A: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5664
Polymers35,3071
Non-polymers2593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9229
Polymers35,3071
Non-polymers6148
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6986
Polymers35,3071
Non-polymers3915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7337
Polymers35,3071
Non-polymers4266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.901, 77.274, 215.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Mandelate racemase/muconate lactonizing enzyme family protein


Mass: 35307.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: Atu1648 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CIT6

-
Non-polymers , 7 types, 723 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mM Tris pH 7.5, 5 mM MgCl, 50 mM L-Ala,L-Glu), Reservoir (0.1 M HEPES:NaOH pH 7.5, 2.0 M Ammonium Sulfate), Cryoprotection (Drop was superconcentrated, no added cryoprotection ...Details: Protein (10 mM Tris pH 7.5, 5 mM MgCl, 50 mM L-Ala,L-Glu), Reservoir (0.1 M HEPES:NaOH pH 7.5, 2.0 M Ammonium Sulfate), Cryoprotection (Drop was superconcentrated, no added cryoprotection required), 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 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2012 / 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: 1.9→107.912 Å / Num. all: 102243 / Num. obs: 102243 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 17.2
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.737 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JPD

1jpd


Resolution: 1.9→62.827 Å / Occupancy max: 1 / Occupancy min: 0.02 / FOM work R set: 0.8573 / SU ML: 0.2 / σ(F): 0 / σ(I): 0 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 5097 4.99 %RANDOM
Rwork0.171 ---
all0.1731 102114 --
obs0.1731 102114 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.01 Å2 / Biso mean: 22.6225 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→62.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9789 0 95 701 10585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810131
X-RAY DIFFRACTIONf_angle_d1.08713798
X-RAY DIFFRACTIONf_chiral_restr0.0711586
X-RAY DIFFRACTIONf_plane_restr0.0051816
X-RAY DIFFRACTIONf_dihedral_angle_d13.6383759
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 (%)
1.9-1.92160.28611560.222332643420100
1.9216-1.94420.29981620.219231953357100
1.9442-1.96790.29241910.207431423333100
1.9679-1.99280.26981530.20332063359100
1.9928-2.0190.22961810.198432053386100
2.019-2.04670.2771800.197831893369100
2.0467-2.0760.27411440.194332213365100
2.076-2.10690.26051710.19331773348100
2.1069-2.13990.25171750.183232423417100
2.1399-2.17490.23871730.179131603333100
2.1749-2.21250.25431520.183232383390100
2.2125-2.25270.2121690.172831523321100
2.2527-2.2960.24171680.176932383406100
2.296-2.34290.23221650.178132213386100
2.3429-2.39380.24961580.18132263384100
2.3938-2.44950.22821790.178431663345100
2.4495-2.51080.23851630.184732353398100
2.5108-2.57870.23171630.182732593422100
2.5787-2.65450.22251920.183232093401100
2.6545-2.74020.21651830.178632023385100
2.7402-2.83820.21911670.181532153382100
2.8382-2.95180.23341810.190832423423100
2.9518-3.08610.24551830.189432313414100
3.0861-3.24880.20661680.180132443412100
3.2488-3.45240.20531580.16732593417100
3.4524-3.71890.18271600.156232743434100
3.7189-4.09310.17971620.143133173479100
4.0931-4.68520.16791830.134632783461100
4.6852-5.90220.17871710.149833603531100
5.9022-62.86140.17091860.16063450363699
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)
10.6428-0.0137-0.30910.69680.07550.9652-0.0229-0.21490.03990.0958-0.06220.0572-0.2398-0.14660.08150.1940.0756-0.02010.38620.02930.1745-17.57669.78011.3296
21.2699-0.4020.31771.018-0.52041.1158-0.09730.06710.0446-0.1869-0.1216-0.0466-0.00850.05680.12110.3113-0.033-0.07430.17410.02560.1253-11.75599.4757-22.9288
30.20560.1854-0.02690.1863-0.19691.5158-0.1028-0.09360.142-0.08770.02360.1355-0.2221-0.18320.05960.19990.0685-0.0640.3501-0.00510.1495-25.24398.5246-12.0496
40.8442-0.2168-0.36970.6399-0.36780.8826-0.0642-0.180.01470.0935-0.017-0.0513-0.04780.0090.03920.11350.0719-0.02790.36470.05010.0975-15.3267-0.17912.9267
50.58730.34670.18280.7812-0.15320.258-0.03350.0803-0.1936-0.10990.0122-0.16730.07960.065-0.01860.1875-0.01980.09830.0221-0.00840.26919.663-13.2178-58.535
60.40420.20490.08390.45130.04130.3714-0.0108-0.0515-0.0130.0349-0.0362-0.0146-0.04450.01890.02550.1234-0.01210.0210.04680.02470.16269.41694.3987-46.1132
70.17970.1682-0.16310.7898-0.20520.15540.0752-0.0676-0.08310.1276-0.0793-0.14580.10850.0696-0.01830.1603-0.0366-0.03970.49220.31750.3964-10.2288-36.23765.5139
80.53510.125-0.03650.23010.07230.2161-0.0277-0.2117-0.11210.0303-0.0709-0.15670.08080.09130.0150.0023-0.03640.03110.47610.22920.2842-16.0864-28.79390.2039
90.94580.3341-0.45371.1596-0.1431.2219-0.0537-0.0229-0.0122-0.1331-0.0118-0.09510.05470.04380.02640.1260.01210.04510.25910.09970.1865-24.0493-30.4585-19.1851
100.53920.05890.09890.16260.06110.08-0.0218-0.1682-0.06860.0122-0.0503-0.00850.0204-0.0396-0.0171-0.011-0.05150.04360.45960.19090.1996-20.4012-24.6582-0.8483
110.90630.0436-0.05920.5402-0.11140.7514-0.01480.13130.1642-0.07750.00390.0395-0.1004-0.16120.00580.17810.0291-0.03180.09970.01580.1469-30.63394.0221-60.7701
121.0842-0.1487-0.24511.36070.29880.9335-0.0195-0.2222-0.02680.0262-0.08810.0174-0.0291-0.07550.09590.0946-0.00410.00620.1402-0.00480.0805-27.5427-10.0918-35.6719
130.79440.0281-0.1210.5518-0.27140.7341-0.0441-0.03770.06220.0496-0.0511-0.0389-0.0281-0.0430.08640.1390.0177-0.010.0602-0.01010.09-22.64120.4187-50.8691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 166 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 218 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 278 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 279 through 327 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 104 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 105 through 327 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 37 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 38 through 166 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 167 through 236 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 237 through 327 )C0
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 123 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 124 through 236 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 237 through 403 )D0

+
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