[English] 日本語
Yorodumi
- PDB-1yl7: the crystal structure of Mycobacterium tuberculosis dihydrodipico... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yl7
Titlethe crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)
ComponentsDihydrodipicolinate reductase4-hydroxy-tetrahydrodipicolinate reductase
KeywordsOXIDOREDUCTASE / lysine biosynthesis / dihydrodipicolinate / reductase / NADH / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 / NADH binding / cell wall / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / NADPH binding / peptidoglycan-based cell wall / plasma membrane / 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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 4-hydroxy-tetrahydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsJanowski, R. / Kefala, G. / Weiss, M.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms.
Authors: Janowski, R. / Kefala, G. / Weiss, M.S.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 30, 2013Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_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: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
C: Dihydrodipicolinate reductase
D: Dihydrodipicolinate reductase
E: Dihydrodipicolinate reductase
F: Dihydrodipicolinate reductase
G: Dihydrodipicolinate reductase
H: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,09522
Polymers205,6268
Non-polymers5,46914
Water6,413356
1
A: Dihydrodipicolinate reductase
B: Dihydrodipicolinate reductase
C: Dihydrodipicolinate reductase
D: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,54811
Polymers102,8134
Non-polymers2,7357
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-105 kcal/mol
Surface area37820 Å2
MethodPISA
2
E: Dihydrodipicolinate reductase
F: Dihydrodipicolinate reductase
G: Dihydrodipicolinate reductase
H: Dihydrodipicolinate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,54811
Polymers102,8134
Non-polymers2,7357
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15770 Å2
ΔGint-106 kcal/mol
Surface area38060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.60, 67.52, 154.49
Angle α, β, γ (deg.)90.00, 117.08, 90.00
Int Tables number5
Space group name H-MC121
DetailsRv2773c occurs as a tetramer. The asymmetric unit contains two independent tetramers ABCD and EFGH.

-
Components

#1: Protein
Dihydrodipicolinate reductase / 4-hydroxy-tetrahydrodipicolinate reductase / DHPR


Mass: 25703.240 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dapB / Plasmid: PETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RP
References: UniProt: P72024, UniProt: P9WP23*PLUS, EC: 1.3.1.26
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris/HCl, 26 % PEG 3350, 140 mM MgCl2 + 3 mM NADH in the protein solution, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8042 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8042 Å / Relative weight: 1
ReflectionResolution: 2.34→99 Å / Num. all: 80382 / Num. obs: 80382 / % possible obs: 86.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 18.9 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 18.7
Reflection shellResolution: 2.34→2.38 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3491 / % possible all: 76.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P9L (MONOMER)

1p9l


Resolution: 2.34→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.937 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.424 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 2428 3 %RANDOM
Rwork0.18134 ---
all0.18307 77923 --
obs0.18307 77923 86.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.528 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-1.04 Å2
2---0.43 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.34→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14428 0 358 356 15142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02215163
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.99820765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59751972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26623.574582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.971152284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.86315107
X-RAY DIFFRACTIONr_chiral_restr0.0830.22504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211355
X-RAY DIFFRACTIONr_nbd_refined0.2020.26831
X-RAY DIFFRACTIONr_nbtor_refined0.3010.210079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2793
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.211
X-RAY DIFFRACTIONr_mcbond_it0.6421.59958
X-RAY DIFFRACTIONr_mcangle_it1.2022.515668
X-RAY DIFFRACTIONr_scbond_it3.31355631
X-RAY DIFFRACTIONr_scangle_it5.141105085
LS refinement shellResolution: 2.34→2.466 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.295 326 -
Rwork0.216 9862 -
obs-2405 76.47 %
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)
12.3073-1.0883-0.06622.4317-0.58893.82670.0483-0.21140.05820.20820.0351-0.34380.16270.5072-0.0834-0.18030.0321-0.03380.02920.0205-0.0363108.0411-12.405227.1
20.58360.23280.03850.9362-0.05871.16590.0113-0.0509-0.0846-0.0773-0.03390.01530.210.04660.0226-0.0610.0340.0088-0.03050.013-0.026585.1928-12.87928.5476
33.10840.3688-0.65963.1493-0.36493.16350.3015-0.24160.28360.3722-0.05580.4256-0.15740.0523-0.2457-0.1044-0.03220.1197-0.2202-0.0549-0.001955.6623-1.9426.7261
40.5043-0.17-0.01920.8889-0.47071.1959-0.0045-0.15390.03240.08940.00760.0303-0.17930.0095-0.003-0.06810.00640.0053-0.0335-0.0332-0.01380.3427.603415.0609
58.98381.64772.39046.9435-0.78397.2383-0.49251.19170.7959-0.57050.1476-1.358-0.64052.16130.3449-0.2498-0.24850.12310.52380.1080.2229110.787815.0282-16.0547
60.08610.1327-0.30371.02720.46972.1418-0.06380.10090.1176-0.0240.0345-0.0783-0.18750.23710.0293-0.0819-0.01510.00250.0007-0.0084-0.005784.877913.581-1.9447
71.61230.4356-0.1110.66830.1082.7337-0.02770.07420.0245-0.10920.01380.03880.159-0.01930.0139-0.0254-0.01270.03-0.1070.0165-0.051860.0706-0.8649-24.8505
80.3416-0.13050.25530.7305-0.08991.1379-0.00650.1045-0.0382-0.11220.03770.01670.19970.0476-0.0312-0.03350.01350.0159-0.01850.0107-0.036484.0704-7.2789-9.0809
92.54490.09870.43594.19880.34512.7362-0.14320.36690.1533-0.21310.1066-0.1475-0.20160.03050.0366-0.0689-0.04450.002-0.0870.0307-0.0924144.805629.445445.9816
101.3743-0.21740.05742.22370.54291.40040.03060.29720.1751-0.2301-0.0342-0.0449-0.0920.04910.0035-0.0413-0.0019-0.0045-0.02920.0696-0.0799120.685236.377555.2603
113.51790.34010.89885.47142.22646.3228-0.1384-0.3914-0.00410.1128-0.20610.2129-0.1697-0.7480.3445-0.22610.0626-0.06570.0358-0.1092-0.144992.745414.683245.323
120.63420.2950.16841.3093-0.20932.3290.10670.1114-0.2628-0.1855-0.02470.07790.3207-0.2191-0.0820.0068-0.0269-0.0134-0.0755-0.0333-0.0544114.526716.789963.4566
131.6606-0.1850.21841.7716-0.34852.95530.04560.04880.05580.05730.0182-0.10860.1430.0657-0.0637-0.05050.04680.0036-0.1166-0.0224-0.0677141.124529.723795.3244
140.93030.25590.16911.18670.04151.34350.0206-0.1068-0.08320.1168-0.0406-0.0210.1918-0.17640.02-0.0103-0.01970.0076-0.02810.0183-0.0668116.700623.959180.3536
157.4263-0.64962.18134.81621.01195.0888-0.5506-0.92111.38810.51890.14280.8724-0.8666-1.68210.4078-0.08080.3311-0.02570.3574-0.02770.264592.491750.587884.969
160.40060.1073-0.03351.79130.18412.4527-0.0464-0.07190.2707-0.0085-0.06920.0123-0.2718-0.19660.1156-0.1060.0128-0.0223-0.09920.0258-0.0154117.567444.290871.5198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1051 - 105
2X-RAY DIFFRACTION1AA218 - 244218 - 244
3X-RAY DIFFRACTION1AO5011
4X-RAY DIFFRACTION2AA106 - 217106 - 217
5X-RAY DIFFRACTION3BB1 - 1051 - 105
6X-RAY DIFFRACTION3BB218 - 244218 - 244
7X-RAY DIFFRACTION3BP5021
8X-RAY DIFFRACTION4BB106 - 217106 - 217
9X-RAY DIFFRACTION5CC1 - 1051 - 105
10X-RAY DIFFRACTION5CC218 - 244218 - 244
11X-RAY DIFFRACTION5CQ5031
12X-RAY DIFFRACTION6CC106 - 217106 - 217
13X-RAY DIFFRACTION7DD1 - 1051 - 105
14X-RAY DIFFRACTION7DD218 - 244218 - 244
15X-RAY DIFFRACTION7DR5041
16X-RAY DIFFRACTION8DD106 - 217106 - 217
17X-RAY DIFFRACTION9EE1 - 1051 - 105
18X-RAY DIFFRACTION9EE218 - 244218 - 244
19X-RAY DIFFRACTION9ES5051
20X-RAY DIFFRACTION10EE106 - 217106 - 217
21X-RAY DIFFRACTION11FF1 - 1051 - 105
22X-RAY DIFFRACTION11FF218 - 244218 - 244
23X-RAY DIFFRACTION11FT5061
24X-RAY DIFFRACTION12FF106 - 217106 - 217
25X-RAY DIFFRACTION13GG1 - 1051 - 105
26X-RAY DIFFRACTION13GG218 - 244218 - 244
27X-RAY DIFFRACTION13GU5071
28X-RAY DIFFRACTION14GG106 - 217106 - 217
29X-RAY DIFFRACTION15HH1 - 1051 - 105
30X-RAY DIFFRACTION15HH218 - 244218 - 244
31X-RAY DIFFRACTION15HV5081
32X-RAY DIFFRACTION16HH106 - 217106 - 217

+
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