[English] 日本語
Yorodumi
- PDB-3p4e: Phosphoribosylformylglycinamidine cyclo-ligase from Vibrio cholerae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p4e
TitlePhosphoribosylformylglycinamidine cyclo-ligase from Vibrio cholerae
ComponentsPhosphoribosylformylglycinamidine cyclo-ligase
KeywordsLIGASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / phosphoribosylaminoimidazole synthetase / PurM / AMP
Function / homology
Function and homology information


purine ribonucleotide biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / cytosol
Similarity search - Function
Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / CITRIC ACID / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsOsipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Phosphoribosylformylglycinamidine cyclo-ligase from Vibrio cholerae.
Authors: Osipiuk, J. / Zhou, M. / Papazisi, L. / Anderson, W.F. / Joachimiak, A.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / 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 / _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: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7785
Polymers37,0841
Non-polymers6944
Water5,080282
1
A: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules

A: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,55510
Polymers74,1682
Non-polymers1,3878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5790 Å2
ΔGint-21 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.277, 106.277, 61.379
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Phosphoribosylformylglycinamidine cyclo-ligase / AIRS / Phosphoribosyl-aminoimidazole synthetase / AIR synthase


Mass: 37084.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar El Tor str. N16961 / Gene: purM, VC2226, VC_2226 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9KPY6, phosphoribosylformylglycinamidine cyclo-ligase

-
Non-polymers , 5 types, 286 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: 0.2 M ammonium-citrate dibasic, 20% PEG 3350, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.77→40.2 Å / Num. all: 39208 / Num. obs: 39208 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.051 / Χ2: 0.91 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.77-1.85.80.6822.0519460.681100
1.8-1.836.80.5719330.696100
1.83-1.8770.44719120.699100
1.87-1.9170.37919620.72100
1.91-1.9570.30119200.762100
1.95-1.9970.23919470.807100
1.99-2.0470.18219670.889100
2.04-2.170.15319160.898100
2.1-2.1670.1319450.96100
2.16-2.2370.11619630.984100
2.23-2.3170.09919591.065100
2.31-2.470.08919351.051100
2.4-2.5170.07819601.061100
2.51-2.6470.06819561.061100
2.64-2.8170.05919630.972100
2.81-3.0370.05219701.01100
3.03-3.336.90.05319781.127100
3.33-3.816.90.05319891.143100
3.81-4.86.70.03320010.967100
4.8-506.70.01720860.58199.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CLI

1cli


Resolution: 1.77→40.17 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.766 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1966 5 %RANDOM
Rwork0.1489 ---
all0.1502 39087 --
obs0.1502 39087 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.13 Å2 / Biso mean: 29.635 Å2 / Biso min: 5.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.29 Å20 Å2
2--0.59 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.77→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 46 282 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222695
X-RAY DIFFRACTIONr_bond_other_d0.0010.021794
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9883691
X-RAY DIFFRACTIONr_angle_other_deg0.9934457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0325.664113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73515477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9371510
X-RAY DIFFRACTIONr_chiral_restr0.1060.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_mcbond_it0.9561.51676
X-RAY DIFFRACTIONr_mcbond_other0.2861.5700
X-RAY DIFFRACTIONr_mcangle_it1.74622714
X-RAY DIFFRACTIONr_scbond_it2.7231019
X-RAY DIFFRACTIONr_scangle_it4.4064.5951
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 150 -
Rwork0.281 2678 -
all-2828 -
obs-2828 98.78 %
Refinement TLS params.Method: refined / Origin x: 35.4502 Å / Origin y: 29.7983 Å / Origin z: 6.5817 Å
111213212223313233
T0.038 Å20.0038 Å20.0079 Å2-0.0107 Å2-0.0021 Å2--0.0129 Å2
L0.8932 °20.0333 °20.2425 °2-0.5692 °2-0.1361 °2--0.607 °2
S0.0269 Å °0.0295 Å °0.0025 Å °-0.0174 Å °-0.0167 Å °0.0753 Å °0.0312 Å °-0.0252 Å °-0.0102 Å °

+
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://pdbjlvh1.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