[English] 日本語
Yorodumi
- PDB-6nnh: Structure of Closed state of Dihydrofolate reductase from Mycobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nnh
TitleStructure of Closed state of Dihydrofolate reductase from Mycobacterium tuberculosis in complex with NADPH and cycloguanil
ComponentsDihydrofolate reductase
KeywordsBIOSYNTHETIC PROTEIN / antifolate
Function / homology
Function and homology information


NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1CY / : / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.523 Å
AuthorsGiudice, J.H.P. / Ribeiro, J.A. / Dias, M.V.B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates.
Authors: Ribeiro, J.A. / Chavez-Pacheco, S.M. / de Oliveira, G.S. / Silva, C.D.S. / Giudice, J.H.P. / Libreros-Zuniga, G.A. / Dias, M.V.B.
History
DepositionJan 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,00714
Polymers35,3222
Non-polymers2,68512
Water6,053336
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0057
Polymers17,6611
Non-polymers1,3446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0017
Polymers17,6611
Non-polymers1,3406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-87 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.319, 71.245, 72.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 23 or resid 25...
21(chain B and (resid 1 through 23 or resid 25...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETARGARG(chain A and (resid 1 through 23 or resid 25...AA1 - 231 - 23
12PROPROPHEPHE(chain A and (resid 1 through 23 or resid 25...AA25 - 3125 - 31
13GLUGLUGLUGLU(chain A and (resid 1 through 23 or resid 25...AA3333
14THRTHRTHRTHR(chain A and (resid 1 through 23 or resid 25...AA35 - 8735 - 87
15PROPROALAALA(chain A and (resid 1 through 23 or resid 25...AA89 - 10789 - 107
16ARGARGARGARG(chain A and (resid 1 through 23 or resid 25...AA109 - 158109 - 158
17SERSERSERSER(chain A and (resid 1 through 23 or resid 25...AA159159
18METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
19METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
110METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
111METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
112METMETSERSER(chain A and (resid 1 through 23 or resid 25...AA1 - 1591 - 159
21METMETARGARG(chain B and (resid 1 through 23 or resid 25...BB1 - 231 - 23
22PROPROPHEPHE(chain B and (resid 1 through 23 or resid 25...BB25 - 3125 - 31
23GLUGLUGLUGLU(chain B and (resid 1 through 23 or resid 25...BB3333
24THRTHRTHRTHR(chain B and (resid 1 through 23 or resid 25...BB35 - 8735 - 87
25PROPROALAALA(chain B and (resid 1 through 23 or resid 25...BB89 - 10789 - 107
26ARGARGSERSER(chain B and (resid 1 through 23 or resid 25...BB109 - 159109 - 159

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Dihydrofolate reductase


Mass: 17660.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: folA, dfrA, Rv2763c, MTV002.28c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WNX1, dihydrofolate reductase

-
Non-polymers , 6 types, 348 molecules

#2: Chemical ChemComp-1CY / 1-(4-chlorophenyl)-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine / Cycloguanil


Mass: 251.715 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14ClN5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.8 M Ammonium sulphate, 10 mM CoCl2, 100 mM MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 1.52→46.3 Å / Num. obs: 47946 / % possible obs: 99.1 % / Redundancy: 11.6 % / Biso Wilson estimate: 13.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.031 / Rrim(I) all: 0.107 / Net I/σ(I): 19.8 / Num. measured all: 557948 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.52-1.5560.89620530.7580.3890.98286.7
8.34-46.37.30.0873570.9870.0330.09399.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
Aimless0.2.8data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NND

6nnd


Resolution: 1.523→10.638 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.4
RfactorNum. reflection% reflection
Rfree0.1986 2346 4.92 %
Rwork0.1696 --
obs0.171 47699 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.15 Å2 / Biso mean: 19.9358 Å2 / Biso min: 7.48 Å2
Refinement stepCycle: final / Resolution: 1.523→10.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 163 336 2986
Biso mean--16.23 31.53 -
Num. residues----318
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A920X-RAY DIFFRACTION6.129TORSIONAL
12B920X-RAY DIFFRACTION6.129TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5227-1.55370.28211270.25072306243387
1.5537-1.58740.25271340.21252562269697
1.5874-1.62420.24831510.190126562807100
1.6242-1.66470.1991390.186226742813100
1.6647-1.70950.22931220.177526652787100
1.7095-1.75960.22351370.170326562793100
1.7596-1.81610.21421390.168126712810100
1.8161-1.88070.19311400.168826792819100
1.8807-1.95550.19151450.161426622807100
1.9555-2.04390.20161360.166226692805100
2.0439-2.15090.17631580.168926782836100
2.1509-2.28440.19761460.167426742820100
2.2844-2.45870.18381390.165727152854100
2.4587-2.70250.22011600.168826692829100
2.7025-3.08520.17211370.171927432880100
3.0852-3.8560.18491200.154627722892100
3.856-10.63850.19551160.167429023018100
Refinement TLS params.Method: refined / Origin x: 22.5412 Å / Origin y: 0.0139 Å / Origin z: 17.6926 Å
111213212223313233
T0.0994 Å2-0.0026 Å2-0.0165 Å2-0.1155 Å2-0.0046 Å2--0.07 Å2
L0.8242 °2-0.2379 °2-0.3968 °2-0.2743 °20.0831 °2--0.1136 °2
S-0.0045 Å °-0.0133 Å °0.0103 Å °-0.0111 Å °0.001 Å °-0.0109 Å °-0.0035 Å °0.0161 Å °0.0051 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allD1 - 2
2X-RAY DIFFRACTION1allA1 - 159
3X-RAY DIFFRACTION1allB1 - 159
4X-RAY DIFFRACTION1allC1 - 2
5X-RAY DIFFRACTION1allE1 - 4
6X-RAY DIFFRACTION1allE5
7X-RAY DIFFRACTION1allF1 - 2
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allS1 - 336

+
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