[English] 日本語
Yorodumi
- PDB-3u54: Crystal structure (Type-1) of SAICAR synthetase from Pyrococcus h... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u54
TitleCrystal structure (Type-1) of SAICAR synthetase from Pyrococcus horikoshii OT3
ComponentsPhosphoribosylaminoimidazole-succinocarboxamide synthase
KeywordsLIGASE / SAICAR synthetase-like fold / ATP-binding / Phosphoribosylaminoimidazole-succinocarboxamide synthetase / PurC / De novo purine biosynthesis / Ligation of carboxy and amine groups
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding
Similarity search - Function
Bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide synthase / : / Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 ...Bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide synthase / : / Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1,4-BUTANEDIOL / : / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsManjunath, K. / Kanaujia, S.P. / Kanagaraj, S. / Jeyakanthan, J. / Sekar, K.
CitationJournal: Int.J.Biol.Macromol. / Year: 2013
Title: Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: insights into thermal stability
Authors: Manjunath, K. / Kanaujia, S.P. / Kanagaraj, S. / Jeyakanthan, J. / Sekar, K.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
B: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,31120
Polymers55,4292
Non-polymers1,88218
Water2,972165
1
A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
B: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules

A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
B: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules

A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
B: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,93460
Polymers166,2876
Non-polymers5,64754
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16350 Å2
ΔGint-432 kcal/mol
Surface area57150 Å2
MethodPISA
2
B: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules

A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,31120
Polymers55,4292
Non-polymers1,88218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4530 Å2
ΔGint-132 kcal/mol
Surface area19860 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-126 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.420, 95.420, 148.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 12 - 233 / Label seq-ID: 12 - 233

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase


Mass: 27714.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0239, purC / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: O57978, phosphoribosylaminoimidazolesuccinocarboxamide synthase

-
Non-polymers , 5 types, 183 molecules

#2: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 293 K / Method: microbatch underoil / pH: 7.5
Details: 0.05M cadmium sulfate hydrate, 0.1M HEPES buffer, 1.0M sodium acetate trihydrate, 40%(w/v) 1,4-butanediol, pH 7.5, MICROBATCH UNDEROIL, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2010 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→55.26 Å / Num. obs: 21057 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.2
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YZL

2yzl


Resolution: 2.35→55.26 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.838 / SU B: 8.865 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.485 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28632 1081 5.1 %RANDOM
Rwork0.23483 ---
obs0.23746 19974 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.812 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.35→55.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 42 165 3736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223622
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9934887
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8375447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.35924.968157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.815650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.611514
X-RAY DIFFRACTIONr_chiral_restr0.080.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212677
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0691.52231
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.99323579
X-RAY DIFFRACTIONr_scbond_it6.23731391
X-RAY DIFFRACTIONr_scangle_it8.1864.51308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1719 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.050.05
tight thermal0.160.5
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 89 -
Rwork0.263 1501 -
obs--100 %

+
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