[English] 日本語
Yorodumi
- PDB-2b1i: crystal structures of transition state analogue inhibitors of ino... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b1i
Titlecrystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase
ComponentsBifunctional purine biosynthesis protein PURH
KeywordsTRANSFERASE / HYDROLASE / ATIC / IMPCH / structure-base / transition state analogue / inhibitor
Function / homology
Function and homology information


De novo synthesis of IMP / phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process / protein homodimerization activity / cytosol
Similarity search - Function
Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily ...Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-93A / : / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsXu, L. / Chong, Y. / Hwang, I. / D'Onofrio, A. / Amore, K. / Beardsley, G.P. / Li, C. / Olson, A.J. / Boger, D.L. / Wilson, I.A.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structure-based Design, Synthesis, Evaluation, and Crystal Structures of Transition State Analogue Inhibitors of Inosine Monophosphate Cyclohydrolase.
Authors: Xu, L. / Chong, Y. / Hwang, I. / D'Onofrio, A. / Amore, K. / Beardsley, G.P. / Li, C. / Olson, A.J. / Boger, D.L. / Wilson, I.A.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of avian AICAR transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening
Authors: Xu, L. / Li, C. / Olson, A.J. / Wilson, I.A.
#2: Journal: J.Med.Chem. / Year: 2004
Title: Successful virtual screening for human AICAR transformylase inhibitors against NCI diversity set using AutoDock.
Authors: Li, C. / Xu, L. / Wolan, D.W. / Wilson, I.A. / Olson, A.J.
#3: Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis
Authors: Greasley, S.E. / Horton, P. / Ramcharan, J. / Beardsley, G.P. / Benkovic, S.J. / Wilson, I.A.
#4: Journal: Biochemistry / Year: 2002
Title: Structural insights into the avian AICAR transformylase mechanism
Authors: Wolan, D.W. / Greasley, S.E. / Beardsley, G.P. / Wilson, I.A.
#5: Journal: Biochemistry / Year: 2003
Title: Structure of avian AICAR transformylase with a multisubstrate adduct inhibitor beta-DADF identifies the folate binding site
Authors: Wolan, D.W. / Greasley, S.E. / Wall, M.J. / Benkovic, S.J. / Wilson, I.A.
#6: Journal: Biochemistry / Year: 2004
Title: Structural insights into the human and avian IMP cyclohydrolase mechanism via crystal structures with the bound XMP Inhibitor
Authors: Wolan, D.W. / Cheong, C.-G. / Greasley, S.E. / Wilson, I.A.
#7: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates
Authors: Cheong, C.G. / Wolan, D.W. / Greasley, S.E. / Horton, P.A. / Beardsley, G.P. / Wilson, I.A.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 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_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.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_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: Bifunctional purine biosynthesis protein PURH
B: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,6758
Polymers128,9952
Non-polymers1,6796
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14660 Å2
ΔGint-72 kcal/mol
Surface area41420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.000, 106.500, 101.000
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer. There is 1 biological unit in the asymmetric unit (chains A & B)

-
Components

#1: Protein Bifunctional purine biosynthesis protein PURH


Mass: 64497.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Includes: Phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase), IMP cyclohydrolase (Inosinicase, IMP synthetase, ATIC)
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ATIC, PURH / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P31335, IMP cyclohydrolase, phosphoribosylaminoimidazolecarboxamide formyltransferase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-93A / [3,4-DIHYDROXY-5R-(2,2,4-TRIOXO-1,2R,3S,4R-TETRAHYDRO-2L6-IMIDAZO[4,5-C][1,2,6]THIADIAZIN-7-YL)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE


Mass: 400.259 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N4O10PS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.3 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 8000, imidazole, DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2004
RadiationMonochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionNumber: 75375 / Rmerge(I) obs: 0.065 / Χ2: 2.621 / D res high: 2.02 Å / D res low: 50 Å / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.355094.510.0535.974
3.454.3596.810.0535.312
3.023.4597.810.0593.497
2.743.0298.210.0732.302
2.542.7498.710.0911.839
2.392.5498.610.1141.544
2.272.399910.1451.375
2.182.2798.610.1721.277
2.092.1897.110.2251.154
2.022.0991.510.2751.105
ReflectionResolution: 2.02→50 Å / Num. obs: 75375 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.065 / Χ2: 2.621 / Net I/σ(I): 24.8
Reflection shellResolution: 2.02→2.09 Å / % possible obs: 91.5 % / Redundancy: 2 % / Mean I/σ(I) obs: 2.8 / Num. measured obs: 7071 / Num. unique all: 7071 / Rsym value: 0.275 / Χ2: 1.105 / % possible all: 91.5

-
Phasing

Phasing MRRfactor: 43.6 / Cor.coef. Fo:Fc: 49.2 / Cor.coef. Io to Ic: 50.3
Highest resolutionLowest resolution
Rotation4 Å20 Å
Translation4 Å15 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G8M

1g8m


Resolution: 2.02→38.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.998 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.194 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1744 2.5 %RANDOM
Rwork0.198 ---
all0.251 75375 --
obs0.199 69574 92.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.161 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å2-0.13 Å2
2--1.91 Å20 Å2
3----4.9 Å2
Refinement stepCycle: LAST / Resolution: 2.02→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9022 0 102 299 9423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229298
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.97712636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88851178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43324.041386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.187151574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8131562
X-RAY DIFFRACTIONr_chiral_restr0.0960.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026934
X-RAY DIFFRACTIONr_nbd_refined0.2240.25679
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2806
X-RAY DIFFRACTIONr_metal_ion_refined0.1780.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3150.26
X-RAY DIFFRACTIONr_mcbond_it0.5461.55878
X-RAY DIFFRACTIONr_mcangle_it0.99929458
X-RAY DIFFRACTIONr_scbond_it1.82833454
X-RAY DIFFRACTIONr_scangle_it2.8554.53178
LS refinement shellResolution: 2.018→2.071 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 115 -
Rwork0.258 4088 -
all-4203 -
obs-4203 83.39 %

+
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