[English] 日本語
Yorodumi
- PDB-2woc: Crystal Structure of the dinitrogenase reductase-activating glyco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2woc
TitleCrystal Structure of the dinitrogenase reductase-activating glycohydrolase (DRAG) from Rhodospirillum rubrum
ComponentsADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
KeywordsHYDROLASE / DIMANGANESE / NITROGEN FIXATION / ADP-RIBOSYLGLYCOHYDROLASE / MONO-ADP-RIBOSYLHYDROLASE
Function / homology
Function and homology information


ADP-ribosyl-[dinitrogen reductase] hydrolase / ADP-ribosyl-[dinitrogen reductase] hydrolase activity / protein de-ADP-ribosylation / nitrogen fixation / metal ion binding / cytoplasm
Similarity search - Function
ADP-ribosyl-dinitrogen reductase hydrolase / ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / : / ADP-ribosyl-[dinitrogen reductase] glycohydrolase
Similarity search - Component
Biological speciesRHODOSPIRILLUM RUBRUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBerthold, C.L. / Wang, H. / Nordlund, S. / Hogbom, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Mechanism of Adp-Ribosylation Removal Revealed by the Structure and Ligand Complexes of the Dimanganese Mono-Adp-Ribosylhydrolase Drag.
Authors: Berthold, C.L. / Wang, H. / Nordlund, S. / Hogbom, M.
History
DepositionJul 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
B: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
C: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,64118
Polymers96,7343
Non-polymers90715
Water6,702372
1
A: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6207
Polymers32,2451
Non-polymers3766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6207
Polymers32,2451
Non-polymers3766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4014
Polymers32,2451
Non-polymers1563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.771, 47.537, 95.212
Angle α, β, γ (deg.)80.84, 86.56, 85.83
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 3 / Auth seq-ID: 3 - 293 / Label seq-ID: 8 - 298

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(-0.408, 0.89, 0.203), (-0.88, -0.323, -0.349), (-0.245, -0.321, 0.915)-30.39517, 57.9845, -20.58209
2given(-0.378, -0.887, -0.265), (0.882, -0.257, -0.395), (0.283, -0.383, 0.88)73.45803, 71.11835, -33.54707

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein ADP-RIBOSYL-[DINITROGEN REDUCTASE] GLYCOHYDROLASE / ADP-RIBOSYLGLYCOHYDROLASE / DINITROGENASE REDUCTASE-ACTIVATING GLYCOHYDROLASE


Mass: 32244.752 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOSPIRILLUM RUBRUM (bacteria) / Strain: S1 / Plasmid: PGEX-6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR(DE3)
References: UniProt: P14300, ADP-ribosyl-[dinitrogen reductase] hydrolase

-
Non-polymers , 5 types, 387 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.02 Å3/Da / Density % sol: 38.61 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.127
DetectorType: CCD / Detector: CCD / Date: Apr 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.2→94.07 Å / Num. obs: 35220 / % possible obs: 89.8 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 58.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.035 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24016 1780 5.1 %RANDOM
Rwork0.17425 ---
obs0.17757 33434 89.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-1.75 Å20.53 Å2
2--0.32 Å20.26 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6612 0 41 372 7025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216796
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9569192
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7845878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8722.799293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.085151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.581559
X-RAY DIFFRACTIONr_chiral_restr0.0820.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025150
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.23524
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.24702
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2340
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2671.54421
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.49826834
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.13532679
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8554.52354
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1160tight positional0.040.05
2B1160tight positional0.040.05
3C1160tight positional0.040.05
1A1022loose positional0.665
2B1022loose positional0.685
3C1022loose positional0.785
1A1160tight thermal0.060.5
2B1160tight thermal0.070.5
3C1160tight thermal0.060.5
1A1022loose thermal1.0810
2B1022loose thermal1.2710
3C1022loose thermal1.1410
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 85 -
Rwork0.221 1501 -
obs--53.67 %
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)
11.4659-0.163-0.55511.8443-0.22931.55760.01930.0420.06070.0798-0.00850.0548-0.057-0.0452-0.0107-0.1263-0.0032-0.0098-0.13160.0103-0.15322.901645.99270.3901
21.23310.7229-0.1333.48170.29671.2424-0.04480.00630.0233-0.2317-0.0030.1253-0.0326-0.05810.0479-0.07160.0023-0.0022-0.13030.0141-0.1793-8.165226.772830.1459
32.39961.25950.05992.03660.27142.5018-0.0506-0.00790.2278-0.15280.01740.0952-0.0655-0.06320.0332-0.122-0.00440.0068-0.0820.0119-0.105814.094656.089558.4549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 293
2X-RAY DIFFRACTION2B3 - 293
3X-RAY DIFFRACTION3C3 - 293

+
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