[English] 日本語
Yorodumi
- PDB-3r11: Crystal structure of NYSGRC enolase target 200555, a putative dip... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r11
TitleCrystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Mg and Fumarate complex
ComponentsEnzyme of enolase superfamily
KeywordsISOMERASE / enolase / structural genomics / putative epimerase / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


racemase and epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / peptide metabolic process / magnesium ion binding
Similarity search - Function
Dipeptide epimerase / 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 ...Dipeptide epimerase / 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
FUMARIC ACID / L-amino acid-D/L-Glu epimerase
Similarity search - Component
Biological speciesFrancisella philomiragia subsp. philomiragia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsVetting, M.W. / Hillerich, B. / Seidel, R.D. / Zencheck, W.D. / Toro, R. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / ...Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / Nair, S.K. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. / Jacobson, M.P.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Mar 28, 2012Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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_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_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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: Enzyme of enolase superfamily
B: Enzyme of enolase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,81112
Polymers84,9102
Non-polymers90110
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-98 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.930, 120.930, 149.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Enzyme of enolase superfamily


Mass: 42455.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella philomiragia subsp. philomiragia (bacteria)
Strain: ATCC 25017 / Gene: Fphi_1647 / Plasmid: CHS30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1R-RIL / References: UniProt: B0TZW0

-
Non-polymers , 5 types, 718 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.2 M Ammonium sulfate, 100 mM MES pH 6.0, 18% ...Details: Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.2 M Ammonium sulfate, 100 mM MES pH 6.0, 18% glycerol, 50mM MgSO4, 50 mM Fumarate, 30 min, vapor diffusion, sitting drop, temperature 294K

-
Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97905 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Details: Undulator Source
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2→93.971 Å / Num. all: 75220 / Num. obs: 75220 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rsym value: 0.111 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.1113.30.4081.8144413108370.408100
2.11-2.2413.40.3052.5137369102720.305100
2.24-2.3913.40.2312.112919796390.231100
2.39-2.5813.50.1782.412159590290.178100
2.58-2.8313.60.138511285583060.138100
2.83-3.1613.80.1264.810440875740.126100
3.16-3.6513.90.1115.49320667010.111100
3.65-4.4714.30.0688.88215957410.068100
4.47-6.3214.40.04613.16491745130.046100
6.32-30.71913.10.03715.43419126080.03799.2

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data processing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→30.323 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9071 / SU ML: 0.16 / σ(F): 0 / Phase error: 15.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 3730 5.02 %random
Rwork0.1498 ---
all0.1513 74238 --
obs0.1513 74238 98.8 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.495 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 84.07 Å2 / Biso mean: 24.7422 Å2 / Biso min: 4.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.3643 Å2-0 Å2-0 Å2
2---0.3643 Å2-0 Å2
3---0.7286 Å2
Refinement stepCycle: LAST / Resolution: 2→30.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5605 0 51 708 6364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085726
X-RAY DIFFRACTIONf_angle_d1.1877744
X-RAY DIFFRACTIONf_chiral_restr0.096916
X-RAY DIFFRACTIONf_plane_restr0.006983
X-RAY DIFFRACTIONf_dihedral_angle_d13.1662099
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02530.21471530.172530268398
2.0253-2.0520.21350.15842536267198
2.052-2.08010.20381200.15462551267198
2.0801-2.10980.19591510.15552531268297
2.1098-2.14130.19951360.15362563269999
2.1413-2.17470.19291320.1462553268598
2.1747-2.21030.19151250.15532590271599
2.2103-2.24840.22621370.15272574271199
2.2484-2.28930.20631300.15172593272398
2.2893-2.33330.18981320.15272585271799
2.3333-2.38090.19251230.14712563268699
2.3809-2.43270.18171410.14462598273999
2.4327-2.48930.18651390.15272571271098
2.4893-2.55150.19831260.15152618274499
2.5515-2.62040.17781330.1472585271899
2.6204-2.69750.19151410.14832608274999
2.6975-2.78450.16851420.15142599274199
2.7845-2.8840.19441570.15112600275799
2.884-2.99930.20261620.154326082770100
2.9993-3.13570.19321440.152726302774100
3.1357-3.30080.18591380.151126512789100
3.3008-3.50730.16111680.141426182786100
3.5073-3.77770.15421400.136326722812100
3.7777-4.1570.16021290.133826962825100
4.157-4.75650.14161320.127327102842100
4.7565-5.98520.15991250.153827622887100
5.9852-30.32650.19911390.18672813295297
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)
10.12120.0360.00620.04690.06360.1010.041-0.06330.03860.0585-0.07070.01990.0328-0.112-0.01170.1196-0.0193-0.02110.1250.01270.100572.90871.803356.8318
20.07140.01270.01240.0080.01940.0657-0.00510.02310.0634-0.01250.01480.00650.0056-0.011-0.0040.0626-0.0097-0.01710.06690.00140.079982.465980.119951.1506
30.01920.00720.00780.00320.00540.0156-0.00530.0186-0.0061-0.03460.00580.01920.0107-0.0310.00780.0716-0.0066-0.0830.0833-0.05450.079871.030772.439941.9888
40.24860.02280.14230.03990.00220.08990.16040.0165-0.44380.00930.0035-0.12870.31610.01920.07890.1759-0.0719-0.1794-0.0196-0.1220.212485.987651.940647.9989
50.0140.0010.00550.0082-0.0040.0038-0.0310.02160.02140.0027-0.01860.0174-0.006-0.0566-0.00330.1727-0.0572-0.10680.2031-0.04110.204263.510364.323650.3043
60.05250.0359-0.03620.0349-0.00870.08550.0819-0.02640.08180.0548-0.02770.00210.0298-0.04360.04940.0853-0.03690.02390.07570.01260.032996.809183.636170.3776
70.0224-0.00440.00280.0138-0.01440.01540.0831-0.0302-0.0280.0693-0.0592-0.00590.081-0.0112-0.00690.1167-0.0349-0.01750.09170.01190.046194.436870.302968.1394
80.0451-0.0441-0.02420.07110.04860.10820.0862-0.01720.07670.0174-0.0109-0.08-0.045-0.0022-0.00340.0739-0.02140.01330.06680.01090.0996108.966985.940864.7206
90.07420.04380.00610.0583-0.0350.05580.09550.04740.0855-0.0923-0.0183-0.0561-0.07140.00350.02850.14670.01810.1160.14880.06450.1461110.53892.931242.269
100.01990.00430.01540.0515-0.0370.05060.02340.02160.0052-0.03880.0163-0.0204-0.00760.0360.02470.1110.01380.06910.17110.00430.0809109.726681.053841.3749
110.0232-0.0136-0.00170.04930.01210.0630.05850.04910.0401-0.0314-0.0164-0.0995-0.01110.0904-0.01640.06070.00950.00640.0881-0.00620.0832109.650574.860453.8221
120.00460.0080.01120.02070.00670.04950.0559-0.00310.03610.01450.0254-0.0118-0.01930.0483-0.02740.0587-0.02610.01170.1103-0.00280.1513110.033387.123664.7136
130.04640.01470.04860.03860.02690.05770.0281-0.05120.01480.0570.0238-0.0467-0.00750.025-0.00320.1264-0.035-0.02510.144-0.03230.1272106.740988.844675.1575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:51)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 52:98)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 99:130)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 131:332)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 333:363)A0
6X-RAY DIFFRACTION6chain 'B' and (resseq 2:51)B0
7X-RAY DIFFRACTION7chain 'B' and (resseq 52:98)B0
8X-RAY DIFFRACTION8chain 'B' and (resseq 99:155)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 156:211)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 212:237)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 238:301)B0
12X-RAY DIFFRACTION12chain 'B' and (resseq 302:332)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 333:365)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