[English] 日本語
Yorodumi
- PDB-4eei: Crystal Structure of Adenylosuccinate Lyase from Francisella tula... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eei
TitleCrystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with AMP and Succinate
ComponentsAdenylosuccinate lyase
KeywordsLYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha structure / AMP binding / beta-elimination / cytosole
Function / homology
Function and homology information


adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
Fumarase/aspartase (C-terminal domain) / Adenylosuccinate lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family ...Fumarase/aspartase (C-terminal domain) / Adenylosuccinate lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / SUCCINIC ACID / Adenylosuccinate lyase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis SCHU S4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.921 Å
AuthorsMaltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Adenylosuccinate Lyase from Francisella tularensis Complexed with AMP and Succinate
Authors: Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 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_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_auth_seq_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.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_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: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,42327
Polymers100,3672
Non-polymers2,05625
Water10,827601
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,84654
Polymers200,7344
Non-polymers4,11250
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area36640 Å2
ΔGint-21 kcal/mol
Surface area59050 Å2
MethodPISA
2
A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,08722
Polymers100,3672
Non-polymers1,72020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10860 Å2
ΔGint0 kcal/mol
Surface area36480 Å2
MethodPISA
3
B: Adenylosuccinate lyase
hetero molecules

B: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,75932
Polymers100,3672
Non-polymers2,39230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area11560 Å2
ΔGint-29 kcal/mol
Surface area36800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.759, 88.759, 254.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-852-

HOH

21B-734-

HOH

31B-871-

HOH

Detailstetramer is generated by applying x,y,z, and y,x,-z+1 to asymmetric unit

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Adenylosuccinate lyase


Mass: 50183.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis SCHU S4 (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: FTT_0015, purB / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q5NIQ1, adenylosuccinate lyase

-
Non-polymers , 6 types, 626 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M succinic acid pH7.0, 0.1M HEPES pH7.0, 1% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 78595 / Num. obs: 78595 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.5
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 15.9 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 4 / Num. unique all: 3857 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1C3U

1c3u


Resolution: 1.921→39.331 Å / SU ML: 0.12 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1893 2.54 %random
Rwork0.168 ---
all0.169 74476 --
obs0.169 74476 94.83 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.97 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.1718 Å20 Å2-0 Å2
2--6.1718 Å2-0 Å2
3----12.3437 Å2
Refinement stepCycle: LAST / Resolution: 1.921→39.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6751 0 127 601 7479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077192
X-RAY DIFFRACTIONf_angle_d0.9929674
X-RAY DIFFRACTIONf_dihedral_angle_d15.5542738
X-RAY DIFFRACTIONf_chiral_restr0.0641081
X-RAY DIFFRACTIONf_plane_restr0.0051237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9214-1.96940.27811260.22084695482187
1.9694-2.02270.26911230.20994803492689
2.0227-2.08220.24671310.20224882501391
2.0822-2.14940.23311250.18854955518092
2.1494-2.22620.21581310.17915028515993
2.2262-2.31540.19841290.1645051518094
2.3154-2.42070.19431360.16695126526295
2.4207-2.54830.21381330.1695147528095
2.5483-2.70790.21881380.17395234537196
2.7079-2.9170.20121390.18535304544397
2.917-3.21040.22111400.17825420556099
3.2104-3.67460.18411440.15654945638100
3.6746-4.62850.15631460.133855955741100
4.6285-39.33930.18631520.16858496001100
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)
10.394-0.0099-0.0050.3585-0.46683.8578-0.0187-0.04-0.05620.09990.02430.1450.0758-0.2549-0.01570.1566-0.00010.06540.1672-0.03040.2337-4.23310.9528142.5484
20.5268-0.120.32020.9554-0.86742.3385-0.00640.0258-0.05680.11280.03780.17430.0224-0.1597-0.03390.12610.00680.04680.1388-0.03850.18962.216112.0193134.8422
31.0212-0.65610.35572.83640.89083.24340.26520.6288-0.1114-0.9847-0.30490.3436-0.1772-0.18030.03650.41730.1064-0.1110.6947-0.04470.3787-12.022415.240790.3477
41.4724-0.54180.63061.0223-0.41181.17470.06270.2232-0.0879-0.0469-0.0716-0.11590.05590.28110.00790.123-0.00250.02030.1898-0.02020.149832.743417.1673117.5873
52.2736-2.2242-0.35795.44492.05583.46040.02650.26630.4141-0.2695-0.30580.5709-1.0936-0.99410.28190.57010.2137-0.06050.50080.09340.5567-3.338156.7301110.3878
62.0081-2.8828-1.66324.35860.83715.49370.01010.14311.0657-0.11940.0231-0.4845-0.45640.5922-0.04360.3823-0.04530.00320.28750.05690.332624.636449.8165111.0763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:173)
2X-RAY DIFFRACTION2chain 'A' and (resseq 174:333)
3X-RAY DIFFRACTION3chain 'A' and (resseq 334:433)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:333)
5X-RAY DIFFRACTION5chain 'B' and (resseq 334:418)
6X-RAY DIFFRACTION6chain 'B' and (resseq 419:438)

+
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