[English] 日本語
Yorodumi
- PDB-1qo2: Crystal structure of N-((5'-phosphoribosyl)-formimino)-5-aminoimi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qo2
TitleCrystal structure of N-((5'-phosphoribosyl)-formimino)-5-aminoimidazol-4-carboxamid ribonucleotid isomerase (EC 3.1.3.15, HisA)
Components
KeywordsISOMERASE / HISTIDINE BIOSYNTHESIS / THERMOPHILIC PROTEIN
Function / homology
Function and homology information


1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA, bacterial-type / Histidine biosynthesis, HisA-like / HisA/PriA, bacterial-type / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsWilmanns, M. / Lang, D. / Thoma, R. / Sterner, R.
Citation
Journal: Science / Year: 2000
Title: Structural Evidence for Evolution of the Beta/Alpha-Barrel Scaffold by Repeated Gene Duplication and Fusion
Authors: Lang, D. / Thoma, R. / Henn-Sax, M. / Sterner, R. / Wilmanns, M.
#1: Journal: FEBS Lett. / Year: 1999
Title: Efficient Expression, Purification and Crystallisation of Two Hyperthermostable Enzymes of Histidine Biosynthesis
Authors: Thoma, R. / Obmolova, G. / Lang, D.A. / Schwander, M. / Jenoe, P. / Sterner, R. / Wilmanns, M.
History
DepositionNov 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A:
B:


Theoretical massNumber of molelcules
Total (without water)54,4182
Polymers54,4182
Non-polymers00
Water9,854547
1
A:


Theoretical massNumber of molelcules
Total (without water)27,2091
Polymers27,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B:


Theoretical massNumber of molelcules
Total (without water)27,2091
Polymers27,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.780, 73.160, 62.700
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9992, -0.01298, -0.03791), (-0.03851, 0.05016, 0.998), (-0.01105, 0.99866, -0.05062)
Vector: 16.28184, -4.59496, 5.49976)

-
Components

#1: Protein / HISA / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE


Mass: 27208.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: M1, M17 AND M236 ARE SELENOMETHIONINE SUBSTITUTED / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Cellular location: CYTOPLASM / Gene: THISA / Plasmid: PDMI, 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 TRPEA2 / References: UniProt: Q9X0C7, D-lyxose ketol-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 1.82 Å3/Da / Density % sol: 31.86 %
Crystal growpH: 5.6
Details: SEE THOMA ET AL. (1999) FEBS LETTERS 454, 1-6., pH 5.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Thoma, R., (1999) FEBS Lett., 454, 1.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
210 mMBis-Tris1drop
31 mMdithiothreitol1drop
41 mMEDTA1drop
529-35 %(w/v)PEG40001reservoir
60.1 Mcitrate1reservoir
7200 mM1reservoirNH4Ac
83 %(v/v)MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.97893, 0.97929, 0.98089
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: RHODIUM COATED PRE-MIRROR FOCUSSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978931
20.979291
30.980891
ReflectionResolution: 1.85→39.841 Å / Num. obs: 34932 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.51 % / Biso Wilson estimate: 27.24 Å2 / Rsym value: 0.041 / Net I/σ(I): 17
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.95 % / Mean I/σ(I) obs: 2.53 / Rsym value: 0.269 / % possible all: 91.9
Reflection
*PLUS
Redundancy: 5.8 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Rmerge(I) obs: 0.304

-
Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
SHARPphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→8 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1707 5 %RANDOM
Rwork0.188 ---
obs0.188 34472 97.4 %-
Solvent computationSolvent model: CNS DEFAULT, ANISOTROPIC B FACTORS
Displacement parametersBiso mean: 20.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.878 Å20 Å2-3.646 Å2
2--5.037 Å20 Å2
3----2.159 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-8 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 0 547 4345
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.31
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.649
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.7889
X-RAY DIFFRACTIONc_mcangle_it1.29312
X-RAY DIFFRACTIONc_scbond_it1.28212
X-RAY DIFFRACTIONc_scangle_it1.98715
LS refinement shellResolution: 1.85→1.87 Å / Total num. of bins used: 34
RfactorNum. reflection% reflection
Rfree0.365 58 5 %
Rwork0.306 855 -
obs--78.64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.31
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.649

+
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