[English] 日本語
Yorodumi
- PDB-1o4u: Crystal structure of a nicotinate nucleotide pyrophosphorylase (t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o4u
TitleCrystal structure of a nicotinate nucleotide pyrophosphorylase (tm1645) from thermotoga maritima at 2.50 A resolution
ComponentsType II quinolic acid phosphoribosyltransferase
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD+ biosynthetic process / cytoplasm
Similarity search - Function
Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 ...Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
nicotinate-nucleotide diphosphorylase (carboxylating)
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution
Authors: Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. ...Authors: Schwarzenbacher, R. / Jaroszewski, L. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type II quinolic acid phosphoribosyltransferase
B: Type II quinolic acid phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)63,3592
Polymers63,3592
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-25 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.371, 126.125, 138.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 273 / Label seq-ID: 13 - 285

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Type II quinolic acid phosphoribosyltransferase


Mass: 31679.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1645 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.57 Å3/Da / Density % sol: 65.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 10% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
410 mg/mlprotein1drop
510 %PEG60001reservoir
60.1 MMES1reservoirpH6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.972386
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2002 / Details: flat mirror
RadiationMonochromator: single crystal Si(111) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972386 Å / Relative weight: 1
ReflectionResolution: 2.501→38.29 Å / Num. all: 29194 / Num. obs: 29194 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 63.66 Å2 / Rsym value: 0.081 / Net I/σ(I): 12.6
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 2002 / Rsym value: 0.546 / % possible all: 93.2
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 125534 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.546

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QPN

1qpn


Resolution: 2.5→38.29 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.677 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. UNEXPLAINED BLOB OF DENSITY AROUND RESIDUE 75 IN BOTH CHAINS, TOO LARGE AND FAR FROM RESIDUES TO BE WATER, NO METALS IN CRYSTALLIZATION SOLUTION. 2. RESIDUAL DENSITY FOR RESIDUE 209 COULD ...Details: 1. UNEXPLAINED BLOB OF DENSITY AROUND RESIDUE 75 IN BOTH CHAINS, TOO LARGE AND FAR FROM RESIDUES TO BE WATER, NO METALS IN CRYSTALLIZATION SOLUTION. 2. RESIDUAL DENSITY FOR RESIDUE 209 COULD NOT BE MODELLED WITHOUT VIOLATING RAMACHANDRAN ANGLES; BUT MODELLED CONFORMATION CORRESPONDS TO HOMOLOGUE 1QPN. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27225 1510 5.2 %RANDOM
Rwork0.21295 ---
obs0.216 27683 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.427 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å20 Å2
2--0.4 Å20 Å2
3----3.88 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 0 113 4187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224132
X-RAY DIFFRACTIONr_bond_other_d0.0010.023988
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9775578
X-RAY DIFFRACTIONr_angle_other_deg0.83539240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6075527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85424.855173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66115784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2281527
X-RAY DIFFRACTIONr_chiral_restr0.0840.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
X-RAY DIFFRACTIONr_nbd_refined0.2250.2833
X-RAY DIFFRACTIONr_nbd_other0.1780.24023
X-RAY DIFFRACTIONr_nbtor_other0.0890.22754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.28
X-RAY DIFFRACTIONr_mcbond_it0.7281.52628
X-RAY DIFFRACTIONr_mcangle_it1.38824250
X-RAY DIFFRACTIONr_scbond_it2.09231504
X-RAY DIFFRACTIONr_scangle_it3.7954.51328
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3991 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.360.5
medium thermal0.452
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 114 5.7 %
Rwork0.33 1886 -
Refinement TLS params.Method: refined / Origin x: 25.6 Å / Origin y: 22.743 Å / Origin z: 41.374 Å
111213212223313233
T0.0311 Å2-0.0072 Å2-0.0555 Å2-0.0583 Å2-0.0097 Å2--0.1054 Å2
L0.2931 °20.124 °20.2731 °2-0.9205 °20.9223 °2--1.0042 °2
S0.119 Å °-0.0258 Å °-0.0888 Å °0.3037 Å °-0.0139 Å °-0.1046 Å °0.3655 Å °-0.0764 Å °-0.1051 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth seq-ID: 1 - 272 / Label seq-ID: 13 - 284

IDAuth asym-IDLabel asym-ID
1AA
2BB
Software
*PLUS
Name: REFMAC / Version: 5.1.9999 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 29193 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.52
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

+
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