[English] 日本語
Yorodumi
- PDB-4bwv: Structure of Adenosine 5-prime-phosphosulfate Reductase apr-b fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bwv
TitleStructure of Adenosine 5-prime-phosphosulfate Reductase apr-b from Physcomitrella Patens
ComponentsPHOSPHOADENOSINE-PHOSPHOSULPHATE REDUCTASE
KeywordsOXIDOREDUCTASE / SULFATE ASSIMILATION / SULFONUCLEOTIDE
Function / homology
Function and homology information


Phosphoadenosine phosphosulphate reductase / Phosphoadenosine phosphosulfate reductase family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phosphoadenosine-phosphosulphate reductase
Similarity search - Component
Biological speciesPHYSCOMITRELLA PATENS (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStevenson, C.E.M. / Hughes, R.K. / McManus, M.T. / Lawson, D.M. / Kopriva, S.
CitationJournal: FEBS Lett. / Year: 2013
Title: The X-Ray Crystal Structure of Apr-B, an Atypical Adenosine 5-Prime-Phosphosulfate Reductase from Physcomitrella Patens
Authors: Stevenson, C.E.M. / Hughes, R.K. / Mcmanus, M.T. / Lawson, D.M. / Kopriva, S.
History
DepositionJul 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.3Dec 20, 2023Group: 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 / pdbx_initial_refinement_model / 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_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: PHOSPHOADENOSINE-PHOSPHOSULPHATE REDUCTASE
B: PHOSPHOADENOSINE-PHOSPHOSULPHATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4254
Polymers64,2122
Non-polymers2122
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint2 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.990, 82.420, 127.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PHOSPHOADENOSINE-PHOSPHOSULPHATE REDUCTASE / ADENOSINE 5-PRIME-PHOSPHOSULFATE REDUCTASE


Mass: 32106.154 Da / Num. of mol.: 2 / Fragment: RESIDUES 65-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSCOMITRELLA PATENS (plant) / Plasmid: PET14B-APR-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8L5D0, adenylyl-sulfate reductase (thioredoxin)
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDI(HYDROXYETHYL)ETHER (PEG): COMPONENT OF PRECIPITANT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALLIZED AT 20 DEGREES C BY HANGING-DROP VAPOUR DIFFUSION USING A PRECIPITANT CONSISTING OF 25% PEG 5000 MME IN 100 MM BIS-TRIS PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→43.53 Å / Num. obs: 54939 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OQ2

2oq2


Resolution: 1.8→37.8 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.829 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19433 2780 5.1 %RANDOM
Rwork0.16255 ---
obs0.16419 52105 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--1.04 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 14 389 4098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193868
X-RAY DIFFRACTIONr_bond_other_d0.0050.023609
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9435240
X-RAY DIFFRACTIONr_angle_other_deg1.10238293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5655470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09323.237207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73215648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2721533
X-RAY DIFFRACTIONr_chiral_restr0.0920.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214402
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02967
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_it1.3991.9111832
X-RAY DIFFRACTIONr_mcbond_other1.3961.911831
X-RAY DIFFRACTIONr_mcangle_it22.8572291
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.122.1612036
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 194 -
Rwork0.31 3819 -
obs--99.53 %
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)
111.7017.1017.66287.496.00778.3240.2024-0.5094-0.34590.4143-0.2621-0.06320.4719-0.40770.05970.09880.00380.04290.11940.03160.044510.18548.733325.0532
24.93072.24070.80225.36140.1251.1877-0.0225-0.55440.21470.6689-0.0888-0.2943-0.27560.04480.11140.159-0.0025-0.07480.2261-0.05340.051115.118124.926933.3846
34.5225-0.17621.09252.4949-1.41076.006-0.1408-0.34040.70790.4533-0.04320.1958-0.7238-0.06910.1840.24210.034-0.06260.1852-0.14850.22029.557638.138831.3434
46.8605-1.80722.71478.876-4.01096.207-0.24850.82151.2641-0.2908-0.16650.1313-0.78440.34910.4150.3895-0.1063-0.12060.30890.07520.530318.030246.143820.8225
52.3252-0.44410.61431.92760.06162.0558-0.118-0.08460.2630.0453-0.0104-0.0738-0.22350.0280.12840.0502-0.0007-0.01960.0901-0.01340.032512.406324.072421.6535
613.782-4.08670.25925.88751.97546.5021-0.34720.42130.5649-0.24920.00020.2688-0.4708-0.27260.34710.08910.0315-0.05510.06590.02030.06765.417224.328611.3804
710.51038.935.197310.77025.88875.65220.265-0.3483-0.4210.577-0.031-0.57170.58930.2429-0.2340.13570.091-0.00860.13070.03830.051518.32133.198119.6157
86.39440.38730.83931.37440.77793.3959-0.0151-0.164-0.6910.240.0320.01410.8149-0.2541-0.01690.2736-0.02630.03050.04950.01320.132410.0431-9.86816.8482
92.61390.64410.54632.41080.28154.56390.04960.2872-0.3284-0.04360.0874-0.03090.460.3039-0.1370.18180.02940.02910.0702-0.07240.127113.7954-10.3374-10.2448
108.65585.5667-4.696610.2781-6.7411.281-0.10660.57940.73-0.33890.36060.3031-0.3569-0.1249-0.2540.194-0.0262-0.01430.1643-0.03370.15726.1386-0.4308-17.4294
111.34380.4171-0.23842.19220.75922.8289-0.10820.0841-0.1027-0.04010.04710.01490.2361-0.07090.06120.06510.00030.01620.02820.01160.025811.90490.86033.5097
128.1609-0.5446-5.13164.4561.97599.973-0.02890.3390.0976-0.55530.2225-0.2155-0.43490.0517-0.19360.1-0.0330.03280.05310.01050.030419.921711.8512-1.0584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A77 - 109
2X-RAY DIFFRACTION2A110 - 144
3X-RAY DIFFRACTION3A145 - 180
4X-RAY DIFFRACTION4A181 - 213
5X-RAY DIFFRACTION5A214 - 289
6X-RAY DIFFRACTION6A290 - 303
7X-RAY DIFFRACTION7B77 - 105
8X-RAY DIFFRACTION8B106 - 139
9X-RAY DIFFRACTION9B140 - 188
10X-RAY DIFFRACTION10B189 - 211
11X-RAY DIFFRACTION11B212 - 285
12X-RAY DIFFRACTION12B286 - 303

+
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