[English] 日本語
Yorodumi
- PDB-7rzo: Crystal structure of a dihydrofolate reductase (folA) from Stenot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rzo
TitleCrystal structure of a dihydrofolate reductase (folA) from Stenotrophomonas maltophilia
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / SSGCID / folA / dihydrofolate reductase / DHFR / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Dihydrofolate reductase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: Crystal Structure of dihydrofolate reductase from Stenotrophomonas maltophilia K279a
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4264
Polymers19,2671
Non-polymers1603
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.170, 104.170, 87.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

-
Components

#1: Protein Dihydrofolate reductase


Mass: 19266.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: folA, Smlt0814 / Plasmid: StmaA.01062.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2FPG1, dihydrofolate reductase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MCSG-1 C7 (313874c7): 100 mM Tris:HCl, pH8.5, 200 mM CaCl2, 25% (w/v) PEG 4000: StmaA.01062.a.B1.PW38724 @ 26.35 mg/mL: 15% EG: puck/pin id: dqg0-6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 5, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→37.66 Å / Num. obs: 22548 / % possible obs: 99.6 % / Redundancy: 9.788 % / Biso Wilson estimate: 32.421 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.057 / Χ2: 1.014 / Net I/σ(I): 24.88 / Num. measured all: 220707 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.859.90.564.2216147164416310.9320.5999.2
1.85-1.99.9360.4365.3815887161215990.9540.45999.2
1.9-1.959.9620.331715372155815430.9720.34999
1.95-2.019.8880.2529.3514901151515070.9810.26699.5
2.01-2.089.9170.19911.514618148014740.990.2199.6
2.08-2.159.930.15214.714021142014120.9920.1699.4
2.15-2.239.8920.12817.3713483136813630.9940.13599.6
2.23-2.329.8790.10420.7213248134713410.9960.1199.6
2.32-2.439.8530.09322.9312612128112800.9970.09899.9
2.43-2.559.8550.08126.0712013122312190.9980.08599.7
2.55-2.689.8720.0729.2511531116911680.9980.07399.9
2.68-2.859.7630.05934.1310876111511140.9980.06299.9
2.85-3.049.8020.0539.6110165103710370.9990.053100
3.04-3.299.6590.04345.294669819800.9990.04599.9
3.29-3.69.630.03651.8786679009000.9990.038100
3.6-4.029.5880.03355.2378818228220.9990.035100
4.02-4.659.5220.03257.269707327320.9990.034100
4.65-5.699.3820.03356.3459486356340.9990.03599.8
5.69-8.059.110.03454.3844914974930.9990.03699.2
8.05-37.668.060.03254.7924103052990.9980.03598

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hi6

5hi6


Resolution: 1.8→37.66 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 1998 8.86 %
Rwork0.1571 20546 -
obs0.1597 22544 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.16 Å2 / Biso mean: 30.5632 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 1.8→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 9 263 1551
Biso mean--38.98 41.67 -
Num. residues----164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.28161380.24051432157099
1.84-1.890.24171420.20621456159899
1.89-1.950.23711380.17641429156799
1.95-2.010.17761440.17351429157399
2.01-2.090.20891360.17471462159899
2.09-2.170.21841270.160514571584100
2.17-2.270.18711390.162914601599100
2.27-2.390.20141450.16514431588100
2.39-2.540.21611480.164614651613100
2.54-2.730.19641540.170914571611100
2.73-3.010.19641580.159814591617100
3.01-3.440.16321490.151814841633100
3.44-4.340.1681300.126315281658100
4.34-37.660.16591500.15531585173599
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)
14.9892-4.2826-2.59753.54492.00216.42490.00450.187-0.2091-0.3464-0.0358-0.24020.14530.1540.15610.2148-0.05740.0390.1726-0.00850.216911.05646.581115.4247
23.87531.7279-0.77314.3045-1.58412.4573-0.0459-0.09620.1189-0.1989-0.1492-0.1225-0.23690.12750.28550.29520.0110.00030.1676-0.01180.24787.927821.551823.471
38.3379-6.3185-6.90335.34896.3388.2385-0.3935-0.5186-0.31040.59120.05820.18270.29230.23090.28890.2373-0.02030.00850.19190.07010.213610.09886.113828.0565
46.5461-2.2151.20883.19983.9388.1456-0.24210.19230.54570.20670.2557-0.7724-0.49790.3850.04910.2492-0.0373-0.00830.22760.0490.244821.686814.402420.928
54.8011-0.5554-0.5662.51132.19612.4191-0.0493-0.23340.09710.07070.1443-0.3687-0.32980.5285-0.06560.2304-0.03040.01020.23890.00190.223426.810710.379120.8168
66.7408-2.2794-1.6082.8679-2.24215.3063-0.1980.1566-0.3978-0.05770.04360.02330.52860.1480.15550.1811-0.02840.02570.1566-0.01780.219120.46642.152914.2105
76.0961.55652.40058.62545.20823.6713-0.29990.55540.2951-0.54670.2514-0.2519-0.51720.4876-0.02710.3012-0.0490.02660.25760.04970.20714.076913.08128.4651
82.91250.716-0.48146.27722.71474.4147-0.04960.09440.2374-0.18080.0230.0717-0.3863-0.10560.0280.19090.0042-0.02310.13820.0370.11915.452817.179318.3183
95.94942.3365-0.99765.91053.58356.6436-0.04140.38730.3778-0.52450.12380.50240.2218-0.2645-0.03180.13070.0226-0.04940.15040.01710.2121-0.63679.76813.4071
100.8828-0.7163-1.09016.93085.72594.531-0.0736-0.0672-0.02260.2506-0.13740.33590.2509-0.11480.21390.1932-0.02990.02030.1834-0.01180.19130.270711.87524.4178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 9 )A0 - 9
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 25 )A10 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 39 )A26 - 39
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 51 )A40 - 51
5X-RAY DIFFRACTION5chain 'A' and (resid 52 through 79 )A52 - 79
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 100 )A80 - 100
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 110 )A101 - 110
8X-RAY DIFFRACTION8chain 'A' and (resid 111 through 129 )A111 - 129
9X-RAY DIFFRACTION9chain 'A' and (resid 130 through 145 )A130 - 145
10X-RAY DIFFRACTION10chain 'A' and (resid 146 through 163 )A146 - 163

+
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://pdbjlvh1.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