[English] 日本語
Yorodumi
- PDB-5ua0: Dimeric crystal structure of HTPA reductase from arabidopsis thaliana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ua0
TitleDimeric crystal structure of HTPA reductase from arabidopsis thaliana
Components4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
KeywordsOXIDOREDUCTASE / HTPA Reductase DHDPR Lysine biosynthesis
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / chloroplast stroma / NADPH binding
Similarity search - Function
Dihydrodipicolinate reductase, plant-type / Dihydrodipicolinate reductase, C-terminal / Dihydrodipicolinate reductase / Dihydrodipicolinate reductase, C-terminus / Dihydrodipicolinate reductase, N-terminal / Dihydrodipicolinate reductase, N-terminus / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKeown, J.K. / Pearce, F.G. / Goldstone, D.C.
CitationJournal: Biochem. J. / Year: 2018
Title: Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly.
Authors: Watkin, S.A.J. / Keown, J.R. / Richards, E. / Goldstone, D.C. / Devenish, S.R.A. / Grant Pearce, F.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
B: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
C: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7905
Polymers107,5973
Non-polymers1922
Water70339
1
A: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic

A: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic


Theoretical massNumber of molelcules
Total (without water)71,7322
Polymers71,7322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3890 Å2
ΔGint-27 kcal/mol
Surface area21610 Å2
MethodPISA
2
B: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
C: 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9244
Polymers71,7322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-49 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.549, 80.620, 92.790
Angle α, β, γ (deg.)90.000, 95.840, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYMETMETAA21 - 29554 - 328
21GLYGLYMETMETBB21 - 29554 - 328
12GLYGLYMETMETAA21 - 29554 - 328
22GLYGLYMETMETCC21 - 29554 - 328
13ASNASNARGARGBB20 - 29653 - 329
23ASNASNARGARGCC20 - 29653 - 329

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein 4-hydroxy-tetrahydrodipicolinate reductase 2, chloroplastic / / HTPA reductase 2


Mass: 35865.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DAPB2, At3g59890, F24G16.160 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8LB01, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.6 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→61.95 Å / Num. obs: 40722 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.042 / Rrim(I) all: 0.114 / Net I/σ(I): 13.6 / Num. measured all: 300898 / Scaling rejects: 110
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.3-2.387.21.8360.499199.8
8.91-61.956.50.0241199

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å54.05 Å
Translation2.3 Å54.05 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.5.7phasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U5I

5u5i


Resolution: 2.3→61.95 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 23.347 / SU ML: 0.241 / SU R Cruickshank DPI: 0.3395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.238
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 2012 4.9 %RANDOM
Rwork0.2261 ---
obs0.2277 38707 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.81 Å2 / Biso mean: 59.756 Å2 / Biso min: 36.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20.26 Å2
2---0.62 Å2-0 Å2
3---0.79 Å2
Refinement stepCycle: final / Resolution: 2.3→61.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5973 0 10 39 6022
Biso mean--75.25 53.84 -
Num. residues----815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196088
X-RAY DIFFRACTIONr_bond_other_d0.0070.025718
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9598264
X-RAY DIFFRACTIONr_angle_other_deg1.259313117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21724.558226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06115950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1291520
X-RAY DIFFRACTIONr_chiral_restr0.080.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216970
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021314
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A282400.05
12B282400.05
21A282080.07
22C282080.07
31B277660.08
32C277660.08
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 162 -
Rwork0.352 2798 -
all-2960 -
obs--99.8 %
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)
110.4057-0.1342-0.38856.8684-1.46126.6353-0.11280.9718-0.6226-0.1376-0.17810.34460.5424-0.36650.29090.2804-0.03140.03580.5411-0.09930.07279.6055101.3519-29.5412
24.0901-0.0876-2.00341.30610.62213.9887-0.02770.45950.0887-0.21210.01130.08020.1023-0.17180.01630.24360.0510.01460.44510.06590.016816.0533108.5048-26.053
36.339-2.0661-4.20544.3323.52185.05290.10670.0195-0.4772-0.6351-0.2287-0.6405-0.20990.64530.1220.34970.11410.1330.82070.19910.346310.383698.31680.7293
42.1885-2.0599-2.9555.92182.2936.37-0.5393-0.3454-0.4960.32330.0109-0.75040.98660.90860.52840.3880.14630.20770.61380.15010.53778.166291.44872.1043
52.57640.993-2.50352.6846-2.8926.4335-0.10160.3465-0.04690.06720.11350.2628-0.2212-0.4718-0.01190.140.06280.01820.4203-0.02720.05334.2408106.9197-13.009
62.8369-1.25811.64383.6034-3.10864.7868-0.143-0.36840.20320.449-0.1801-0.4182-0.31110.27740.32310.35760.0051-0.00350.53660.01140.059645.266684.44770.6832
72.7938-2.2444-0.04074.2666-2.97427.19580.13580.19930.0381-0.0958-0.04740.08240.7068-0.1838-0.08830.27720.0189-0.02450.38830.00010.018837.362380.5534-11.1014
81.0898-0.2691-0.172.22170.14345.0371-0.2742-0.1536-0.2947-0.0069-0.0443-0.45190.28490.27970.31850.31480.06310.17290.29590.08050.243845.75992.1274-32.8655
91.5850.7801-1.15421.2187-2.06096.1751-0.2208-0.2175-0.00430.035-0.427-0.6105-0.25891.01890.64790.31460.02390.00020.49290.18590.541553.720697.7042-27.5032
108.18050.5324-1.34087.3713-3.80618.64960.2012-0.49740.36860.09710.01590.4484-0.4147-0.5458-0.21710.16750.10740.02470.4811-0.00640.043331.803191.4501-11.6581
113.8371-1.42721.02127.254-3.27096.3845-0.09220.20250.0321-0.8593-0.2458-0.37640.20330.1190.33810.5132-0.01060.1620.3935-0.0030.063338.8123108.1096-63.0809
121.6436-0.0787-0.29516.253-0.94024.49780.0420.33-0.0189-0.29380.13870.34880.063-0.4182-0.18080.4037-0.02260.06570.41290.03910.04428.1475113.341-59.5443
131.837-0.28270.80641.7836-0.70715.5897-0.29360.08320.4376-0.03460.0727-0.2144-0.3594-0.13110.2210.38290.03470.02610.23310.03140.141336.3336105.6418-35.1091
143.50152.9786-0.28858.4075-0.4730.7561-0.06780.62781.0740.160.2184-0.3074-0.8862-0.0351-0.15051.10050.03350.04140.42950.13810.646439.881112.6067-30.7117
150.2529-0.7518-0.26859.5932-1.81042.16460.1689-0.29950.23570.26740.01110.0314-1.46160.5983-0.181.2424-0.3451-0.1660.87070.02360.854.7901114.3257-28.2078
163.3289-0.39812.49461.8323-1.70936.0203-0.00510.0636-0.0882-0.1799-0.059-0.40860.1334-0.14370.06410.37680.02050.14110.23230.03010.14139.7731102.9879-41.848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 43
2X-RAY DIFFRACTION2A44 - 160
3X-RAY DIFFRACTION3A161 - 191
4X-RAY DIFFRACTION4A192 - 238
5X-RAY DIFFRACTION5A239 - 295
6X-RAY DIFFRACTION6B20 - 127
7X-RAY DIFFRACTION7B128 - 147
8X-RAY DIFFRACTION8B148 - 205
9X-RAY DIFFRACTION9B206 - 272
10X-RAY DIFFRACTION10B273 - 296
11X-RAY DIFFRACTION11C17 - 64
12X-RAY DIFFRACTION12C65 - 134
13X-RAY DIFFRACTION13C135 - 178
14X-RAY DIFFRACTION14C179 - 205
15X-RAY DIFFRACTION15C206 - 228
16X-RAY DIFFRACTION16C229 - 296

+
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