[English] 日本語
Yorodumi
- PDB-3rtb: Crystal structure of tm0922, a fusion of a domain of unknown func... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rtb
TitleCrystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Adenosine-3'-5'-Diphosphate
Components
  • Putative uncharacterized protein
  • Unknown peptide, probably from expression host
KeywordsLYASE / Unknown function / ADP/ATP-dependent NAD(P)H-hydrate dehydratase
Function / homology
Function and homology information


NAD(P)H-hydrate epimerase / ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / NAD(P)HX epimerase activity / metabolite repair / nicotinamide nucleotide metabolic process / ATP binding / metal ion binding
Similarity search - Function
Bifunctional NAD(P)H-hydrate repair enzyme Nnr / YjeF N-terminal domain / YjeF C-terminal domain signature 1. / Carbohydrate kinase, predicted, conserved site / YjeF C-terminal domain signature 2. / ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / NAD(P)H-hydrate dehydratase / YjeF C-terminal domain profile. / YjeF-related protein N-terminus / YjeF N-terminal domain ...Bifunctional NAD(P)H-hydrate repair enzyme Nnr / YjeF N-terminal domain / YjeF C-terminal domain signature 1. / Carbohydrate kinase, predicted, conserved site / YjeF C-terminal domain signature 2. / ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase / NAD(P)H-hydrate dehydratase / YjeF C-terminal domain profile. / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / : / Bifunctional NAD(P)H-hydrate repair enzyme Nnr
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShumilin, I.A. / Cymborowski, M. / Lesley, S.A. / Minor, W.
CitationJournal: Structure / Year: 2012
Title: Identification of unknown protein function using metabolite cocktail screening.
Authors: Shumilin, I.A. / Cymborowski, M. / Chertihin, O. / Jha, K.N. / Herr, J.C. / Lesley, S.A. / Joachimiak, A. / Minor, W.
History
DepositionMay 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: Unknown peptide, probably from expression host
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8225
Polymers55,2632
Non-polymers5583
Water3,009167
1
A: Putative uncharacterized protein
B: Unknown peptide, probably from expression host
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)446,57540
Polymers442,10816
Non-polymers4,46724
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area49840 Å2
ΔGint-124 kcal/mol
Surface area134570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.943, 121.943, 155.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Putative uncharacterized protein


Mass: 54527.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0922, TM_0922 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X024, ATP-dependent NAD(P)H-hydrate dehydratase
#2: Protein/peptide Unknown peptide, probably from expression host


Mass: 735.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Unknown peptide, probably from expression host / Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3)

-
Non-polymers , 4 types, 170 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Na Cacodylate, 1.6 M Na Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2009 / Details: BERYLLIUM LENSES
Diffraction measurementDetails: 1.00 degrees, 6.4 sec, detector distance 190.00 mm / Method: \w scans
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionAv R equivalents: 0.088 / Number: 351421
ReflectionResolution: 2.1→50 Å / Num. all: 34690 / Num. obs: 34567 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 24.754
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 2.102 / Rsym value: 0.891 / % possible all: 100
Cell measurementReflection used: 351421

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AX3

2ax3


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.829 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20538 1735 5 %RANDOM
Rwork0.16231 ---
obs0.1645 32709 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.824 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 34 167 3978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223906
X-RAY DIFFRACTIONr_bond_other_d00.022634
X-RAY DIFFRACTIONr_angle_refined_deg1.7772.0075295
X-RAY DIFFRACTIONr_angle_other_deg4.18436471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.724.575153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0715685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8791521
X-RAY DIFFRACTIONr_chiral_restr0.1070.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214275
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02744
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_it0.8811.52449
X-RAY DIFFRACTIONr_mcbond_other01.51022
X-RAY DIFFRACTIONr_mcangle_it1.62223953
X-RAY DIFFRACTIONr_scbond_it2.90731457
X-RAY DIFFRACTIONr_scangle_it4.8234.51341
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 125 -
Rwork0.2 2379 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.38452.33110.54453.9459-0.66123.8713-0.12470.29040.1964-0.10850.21380.18850.2108-0.2059-0.08910.0118-0.0059-0.00680.17650.06560.0369-46.611.503-7.461
21.76890.59410.2523.7751-1.47844.7075-0.1477-0.08050.2320.37730.2960.106-0.8209-0.3949-0.14830.13820.10030.01970.11250.03180.0725-46.54117.869-3.778
30.84060.2188-0.1981.5267-0.71913.7648-0.03350.04270.1118-0.1081-0.0194-0.0442-0.0378-0.13140.05290.0011-0.00370.01020.11160.04140.1122-40.51510.814-18.228
417.3553-12.5909-2.259215.298-1.42012.8071-0.3473-0.6797-0.7891.12530.00330.65940.040.18870.34390.1839-0.04450.05520.16310.1130.173-27.697-10.782-23.914
50.6452-0.4210.59312.7944-1.22951.51310.0243-0.0215-0.0923-0.12130.10010.1620.0863-0.0412-0.12430.04920.0032-0.01610.05250.01290.1176-14.647-11.67-41.818
62.11020.02460.07931.22120.08771.65910.04590.3487-0.0719-0.26090.01130.13370.0233-0.0888-0.05710.09710.0014-0.04680.065-0.00530.0573-20.059-6.853-54.196
70.9109-0.19540.03521.11650.23680.78720.0487-0.0116-0.0823-0.02070.01120.1585-0.0037-0.1689-0.05990.0352-0.00090.00360.08240.05220.1277-29.405-1.133-36.861
84.47463.5736-4.003414.2133-14.974516.80520.0296-0.3202-0.02760.4523-0.0162-0.0658-0.2590.1659-0.01340.0920.02370.00380.09880.00330.1508-13.791-5.166-26.39
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 37
2X-RAY DIFFRACTION2A38 - 122
3X-RAY DIFFRACTION3A123 - 208
4X-RAY DIFFRACTION4A209 - 222
5X-RAY DIFFRACTION5A223 - 264
6X-RAY DIFFRACTION6A265 - 352
7X-RAY DIFFRACTION7A353 - 475
8X-RAY DIFFRACTION8A476 - 489

+
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