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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rrb
TitleCrystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with AMP
Components
  • Bifunctional NAD(P)H-hydrate repair enzyme Nnr
  • peptide
KeywordsLYASE / Unknown function / ADP/ATP-dependent NAD(P)H-hydrate dehydratase
Function / homology
Function and homology information


NAD(P)H-hydrate epimerase / metabolite repair / ADP-dependent NAD(P)H-hydrate dehydratase / ADP-dependent NAD(P)H-hydrate dehydratase activity / NADHX epimerase activity / NADPHX epimerase activity / 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 / Carbohydrate kinase / YjeF C-terminal domain profile. / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus ...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 / Carbohydrate kinase / YjeF C-terminal domain profile. / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / 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 MONOPHOSPHATE / : / 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: 2.4 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
DepositionApr 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / entity / entity_src_gen / entity_src_nat / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional NAD(P)H-hydrate repair enzyme Nnr
B: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9975
Polymers55,2632
Non-polymers7343
Water68538
1
A: Bifunctional NAD(P)H-hydrate repair enzyme Nnr
B: peptide
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)447,97640
Polymers442,10816
Non-polymers5,86824
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 area40330 Å2
ΔGint-140 kcal/mol
Surface area140220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.102, 122.102, 155.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Bifunctional NAD(P)H-hydrate repair enzyme Nnr


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: nnr / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X024
#2: Protein/peptide peptide


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)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 53.12 %
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-D / Wavelength: 1.12712 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12712 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 200896 / Num. obs: 200896 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 38.523
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.938 / Mean I/σ(I) obs: 1.814 / Rsym value: 0.938 / % possible all: 98.9

-
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: 2.4→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.18 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1193 5.2 %RANDOM
Rwork0.167 ---
obs0.17 23145 99.49 %-
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 max: 120.84 Å2 / Biso mean: 58.275 Å2 / Biso min: 34.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 47 38 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223883
X-RAY DIFFRACTIONr_bond_other_d00.022622
X-RAY DIFFRACTIONr_angle_refined_deg1.7062.0045261
X-RAY DIFFRACTIONr_angle_other_deg4.2236442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3295493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86324.539152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56215684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0371521
X-RAY DIFFRACTIONr_chiral_restr0.0960.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214257
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02741
X-RAY DIFFRACTIONr_mcbond_it0.7521.52442
X-RAY DIFFRACTIONr_mcbond_other01.51019
X-RAY DIFFRACTIONr_mcangle_it1.47123942
X-RAY DIFFRACTIONr_scbond_it2.53331441
X-RAY DIFFRACTIONr_scangle_it4.2224.51319
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 109 -
Rwork0.268 1548 -
all-1657 -
obs--98.05 %
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)
119.2997-3.6037-15.216118.0938-11.753920.2624-0.1426-0.99820.82831.58640.40620.9179-1.16320.6979-0.26370.6659-0.23140.15820.2374-0.18690.24383.97254.66715.032
23.2969-0.2698-1.20692.40740.06484.68620.24840.4012-0.0134-0.0308-0.15820.1992-0.4593-0.4495-0.09020.26240.0710.06030.08410.0040.063-12.22445.752.887
34.9413-1.6465-3.6671.08620.16316.18830.25750.49340.19290.06370.03040.4209-0.6682-1.2646-0.28790.25270.14910.07620.2180.05010.289-21.4646.7797.891
41.49550.1044-1.04581.1334-0.22683.9185-0.1207-0.1406-0.05610.096-0.02230.0995-0.21510.07080.14290.2485-0.0120.07290.03810.02180.1638-9.22639.57118.392
58.26-4.02541.82275.17590.13590.25650.50610.55020.5094-0.5556-0.3324-0.62690.13050.1244-0.17370.1863-0.04240.17210.1571-0.02630.199117.68220.18928.027
61.5198-0.167-0.0182.53190.03472.0490.0408-0.29920.13330.31630.0589-0.159-0.0638-0.0224-0.09980.16-0.00080.0190.1918-0.06230.09516.81818.54752.213
71.4857-0.37320.15691.4439-0.02981.40660.0054-0.04620.23210.00870.1157-0.1104-0.24560.0048-0.12110.18650.00250.0890.1142-0.00230.16241.20429.54437.169
819.63840.714-21.22354.2226-4.071425.46950.20310.6113-0.0122-0.5652-0.01640.35320.2433-0.3887-0.18670.1838-0.00760.01180.1513-0.01580.11555.23213.50426.192
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 13
2X-RAY DIFFRACTION2A14 - 88
3X-RAY DIFFRACTION3A89 - 129
4X-RAY DIFFRACTION4A130 - 210
5X-RAY DIFFRACTION5A211 - 233
6X-RAY DIFFRACTION6A234 - 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://pdbjlvh1.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