[English] 日本語
Yorodumi
- PDB-5tek: Apo Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tek
TitleApo Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis
Components4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / Lysine Biosynthesis
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate reductase / oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor / 4-hydroxy-tetrahydrodipicolinate reductase / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / cytosol
Similarity search - Function
Dihydrodipicolinate reductase, conserved site / Dihydrodipicolinate reductase signature. / 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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMank, N. / Pote, S. / Arnette, K. / Klapper, V. / Chruszcz, M.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Authors: Pote, S. / Kachhap, S. / Mank, N.J. / Daneshian, L. / Klapper, V. / Pye, S. / Arnette, A.K. / Shimizu, L.S. / Borowski, T. / Chruszcz, M.
History
DepositionSep 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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
B: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9009
Polymers52,3592
Non-polymers5417
Water2,900161
1
A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules

A: 4-hydroxy-tetrahydrodipicolinate reductase
B: 4-hydroxy-tetrahydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,80118
Polymers104,7194
Non-polymers1,08214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area15040 Å2
ΔGint-132 kcal/mol
Surface area39360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.569, 122.607, 80.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 0 - 244 / Label seq-ID: 4 - 248

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

-
Components

#1: Protein 4-hydroxy-tetrahydrodipicolinate reductase / HTPA reductase


Mass: 26179.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: dapB, MRA_2798 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5U6C6, 4-hydroxy-tetrahydrodipicolinate reductase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium Chloride, 0.1 M HEPES pH 7.5, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 40777 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/av σ(I): 42.383 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.034.80.6550.856199.3
2.03-2.075.30.5830.9071100
2.07-2.115.70.4770.9341100
2.11-2.155.70.4360.9291100
2.15-2.25.70.3550.961100
2.2-2.255.60.3330.9481100
2.25-2.315.70.2580.9731100
2.31-2.375.70.2010.9851100
2.37-2.445.70.1650.9841100
2.44-2.525.70.1390.9891100
2.52-2.615.70.1190.9921100
2.61-2.715.70.1020.9931100
2.71-2.845.70.0910.9941100
2.84-2.995.60.0760.9961100
2.99-3.175.60.0660.997199.9
3.17-3.425.50.060.997199.7
3.42-3.765.40.0520.998199.8
3.76-4.315.30.0480.998199
4.31-5.425.40.0440.998198.8
5.42-404.90.0490.994196.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YL5

1yl5


Resolution: 2.01→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.139
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 2023 5 %RANDOM
Rwork0.192 ---
obs0.1932 38724 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.29 Å2 / Biso mean: 55.381 Å2 / Biso min: 31.13 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å20 Å2
2---1.4 Å20 Å2
3----2.27 Å2
Refinement stepCycle: final / Resolution: 2.01→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 22 161 3822
Biso mean--71.18 60.45 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193723
X-RAY DIFFRACTIONr_bond_other_d00.023635
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9685070
X-RAY DIFFRACTIONr_angle_other_deg3.74538337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5615494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27923.681144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89815564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1141525
X-RAY DIFFRACTIONr_chiral_restr0.080.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214235
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02796
X-RAY DIFFRACTIONr_mcbond_it1.8113.4941982
X-RAY DIFFRACTIONr_mcbond_other1.813.4921981
X-RAY DIFFRACTIONr_mcangle_it2.8025.2282474
Refine LS restraints NCS

Ens-ID: 1 / Number: 27680 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 110 -
Rwork0.349 2604 -
all-2714 -
obs--90.86 %
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)
15.1113-0.6647-1.91658.04490.14540.73030.4494-0.65990.22960.0436-0.3677-0.9116-0.2280.2602-0.08160.5204-0.1701-0.03020.4101-0.02260.1717-3.64131.66511.25
23.5197-0.63370.30272.82011.32256.28420.0414-0.1311-0.0288-0.1461-0.24220.3280.325-0.38290.20090.08360.019-0.02060.1394-0.03260.0428-18.97719.825.985
31.6303-0.8228-0.5024.3939-0.21951.4992-0.0791-0.045-0.25480.30830.13550.7353-0.2804-0.4506-0.05640.10740.08320.05550.20090.05660.1423-14.2583.956-21.128
43.6555-2.8511-2.56493.14473.52745.47560.17370.00470.1377-0.3848-0.0837-0.1004-0.11370.2128-0.090.26120.087-0.0070.24540.01930.0089-10.44419.837-4.622
52.5695-0.2541.68763.9496-1.12436.0037-0.08890.3708-0.125-0.2590.0612-0.05450.44950.25860.02780.1311-0.00140.00210.2155-0.03210.0133-5.44521.638-54.187
61.83541.08090.06472.48370.28873.1513-0.20090.15160.12080.06410.1232-0.1134-0.24070.47310.07770.0921-0.0096-0.03920.1984-0.00310.06780.77630.833-43.486
73.1221-1.5466-1.48272.6265-0.48073.4940.05850.15530.49980.1424-0.1586-0.5941-0.55440.12640.10.2227-0.0539-0.0290.0872-0.01430.23055.64815.908-23.972
82.0799-1.741-0.43834.21280.26142.4639-0.0363-0.13870.52540.2536-0.0057-0.9844-0.2440.40170.0420.1237-0.0768-0.0570.1481-0.05670.313211.75410.337-19.606
90.663-0.6390.69083.5052-3.2553.0471-0.0563-0.04660.09850.20420.12430.084-0.1624-0.1045-0.0680.24340.07960.0130.1894-0.02320.074-6.08518.713-33.201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 3
2X-RAY DIFFRACTION2A4 - 107
3X-RAY DIFFRACTION3A108 - 211
4X-RAY DIFFRACTION4A212 - 245
5X-RAY DIFFRACTION5B0 - 51
6X-RAY DIFFRACTION6B52 - 112
7X-RAY DIFFRACTION7B113 - 157
8X-RAY DIFFRACTION8B158 - 201
9X-RAY DIFFRACTION9B202 - 246

+
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