[English] 日本語
Yorodumi
- PDB-4x5f: ecDHFR complexed with folate and NADP+ at 0.1 MPa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x5f
TitleecDHFR complexed with folate and NADP+ at 0.1 MPa
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / 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
BETA-MERCAPTOETHANOL / FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsYamada, H. / Watanabe, N. / Nagae, T.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP.
Authors: Nagae, T. / Yamada, H. / Watanabe, N.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.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)39,1298
Polymers36,6032
Non-polymers2,5266
Water3,909217
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5654
Polymers18,3021
Non-polymers1,2633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5654
Polymers18,3021
Non-polymers1,2633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.956, 59.926, 72.320
Angle α, β, γ (deg.)90.00, 102.82, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Dihydrofolate reductase


Mass: 18301.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N7O6
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 6000, imidazole, calcium chloride

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 35866 / % possible obs: 95.9 % / Redundancy: 4.1 % / Net I/σ(I): 20.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.924 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18974 1696 4.9 %RANDOM
Rwork0.15233 ---
obs0.15413 32606 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.902 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0 Å20.16 Å2
2--0.04 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 162 217 2925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192789
X-RAY DIFFRACTIONr_bond_other_d0.0010.022504
X-RAY DIFFRACTIONr_angle_refined_deg2.2832.0123813
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0015760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32924.031129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29715423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1331518
X-RAY DIFFRACTIONr_chiral_restr0.1460.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213107
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02661
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_it2.0981.8011280
X-RAY DIFFRACTIONr_mcbond_other2.0941.81278
X-RAY DIFFRACTIONr_mcangle_it2.9242.6921593
X-RAY DIFFRACTIONr_mcangle_other2.9252.6921593
X-RAY DIFFRACTIONr_scbond_it4.0262.3131509
X-RAY DIFFRACTIONr_scbond_other4.0252.3141510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1113.2752221
X-RAY DIFFRACTIONr_long_range_B_refined7.75516.4863182
X-RAY DIFFRACTIONr_long_range_B_other7.7316.2573142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 112 -
Rwork0.241 1943 -
obs--78.8 %

+
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