[English] 日本語
Yorodumi
- PDB-4eig: CA1698 camel antibody fragment in complex with DHFR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eig
TitleCA1698 camel antibody fragment in complex with DHFR
Components
  • CA1698 camel antibody fragment
  • Dihydrofolate reductase
KeywordsOXIDOREDUCTASE/IMMUNE SYSTEM / NADP binding / OXIDOREDUCTASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 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 / Immunoglobulins ...Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOyen, D. / Srinivasan, V.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Mechanistic analysis of allosteric and non-allosteric effects arising from nanobody binding to two epitopes of the dihyrofolate reductase of Escherichia coli.
Authors: Oyen, D. / Wechselberger, R. / Srinivasan, V. / Steyaert, J. / Barlow, J.N.
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrofolate reductase
B: CA1698 camel antibody fragment


Theoretical massNumber of molelcules
Total (without water)31,6452
Polymers31,6452
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-7 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.270, 72.270, 140.371
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Dihydrofolate reductase /


Mass: 18019.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Antibody CA1698 camel antibody fragment


Mass: 13625.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG w/v 1500, 0.1M Tris, 0.1M Ammonium Sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2011
RadiationMonochromator: monochromator (horizontally side diffracting Silicon 111 crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→37.475 Å / Num. obs: 14192 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.64 Å / % possible all: 98.5

-
Processing

Software
NameVersionClassification
MAR345225data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→37.475 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 715 5.04 %
Rwork0.1722 --
obs0.1744 14192 98.89 %
all-14351 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.177 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.871 Å20 Å20 Å2
2--1.871 Å2-0 Å2
3----3.742 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 0 84 2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082158
X-RAY DIFFRACTIONf_angle_d1.092937
X-RAY DIFFRACTIONf_dihedral_angle_d13.103765
X-RAY DIFFRACTIONf_chiral_restr0.074328
X-RAY DIFFRACTIONf_plane_restr0.004380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.69330.27491470.20582670X-RAY DIFFRACTION98
2.6933-2.96430.26491540.19342652X-RAY DIFFRACTION99
2.9643-3.3930.24271520.17232683X-RAY DIFFRACTION99
3.393-4.27380.19111210.1672739X-RAY DIFFRACTION99
4.2738-37.47960.19241410.16072733X-RAY DIFFRACTION99
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)
11.30510.37750.34492.26162.05413.43470.0184-0.20640.11710.2909-0.0347-0.1803-0.2858-0.09210.03490.3845-0.0274-0.12980.0909-0.04130.206623.539115.929316.5912
24.8059-1.36050.88666.38382.88161.86220.1696-0.78780.27770.9475-0.21030.0759-0.4123-0.28420.02760.6694-0.0555-0.04990.2833-0.05590.21621.401514.408431.8658
30.43160.1606-0.04730.98561.34762.06990.0376-0.1840.38410.1948-0.09420.0345-0.5218-0.13940.26740.63390.0603-0.11230.1609-0.10110.326320.554823.895817.275
42.45082.8605-0.74423.97450.42192.8398-0.0288-0.12450.50.1003-0.09530.4863-0.8697-0.0591-0.03451.0435-0.0862-0.20580.27440.02120.402629.110129.81498.5421
53.3981.39520.34547.37383.28792.039-0.0537-0.07770.3580.2120.1011-0.383-0.56690.1311-0.15660.5425-0.0613-0.06010.13560.06610.290929.269520.73246.2667
66.29521.0916-3.00532.1553-1.38141.81110.397-0.6466-0.86941.37820.2122-1.35291.52041.6408-0.63340.5640.1261-0.13960.32920.04950.399228.6916-10.835311.0891
70.7221-0.72530.81231.3064-1.09151.1510.14660.17050.0025-0.3541-0.1383-0.01570.09130.0702-0.02910.70140.234-0.06620.3003-0.05730.220726.963-13.4631-10.8082
81.2695-1.0458-2.38072.26872.50757.5453-0.20540.0241-0.3403-0.1623-0.26120.0420.4904-0.16260.41390.3185-0.0305-0.07940.09610.00940.287121.1927-7.359810.2756
95.3708-2.4059-4.7534.51871.17154.76640.3319-0.56670.2511-0.28690.0838-1.3494-0.04341.1819-0.37940.21230.024-0.01680.3391-0.06990.450632.1788-0.66691.7607
107.6552-3.0577-6.64825.60532.81897.90710.37360.29960.4709-0.2684-0.27290.2153-0.6337-0.2992-0.20790.28440.0248-0.04630.0887-0.01990.191920.15393.08684.1827
112.7197-1.2125-1.37830.96632.15096.50470.02420.09810.3688-0.24850.01190.16230.0562-0.3299-0.05860.2492-0.0493-0.08520.1006-0.02710.233419.2064-1.1778-0.6978
124.37923.2947-5.06258.3257-6.37337.0338-0.03620.2656-0.1266-0.4470.19380.65990.8094-0.3359-0.13830.26540.0026-0.09050.08280.00080.295919.6717-7.9072.2049
135.27-0.23424.49588.70063.89335.76310.57831.47020.1211-1.4736-0.2869-0.28-0.45590.6426-0.31940.580.16850.07430.3932-0.02810.250928.1311-5.4719-11.9835
147.9765-4.5856-6.30976.335.64646.32530.3531-0.1063-0.07710.1407-0.0925-0.38510.21530.2041-0.3050.19640.0098-0.05130.1663-0.00670.267229.875-3.72084.696
152.0686-1.2087-0.81555.06452.93265.26370.24710.1199-0.0572-0.1268-0.1983-0.50480.41620.0765-0.30490.24010.0419-0.11180.1275-0.00320.361529.9975-4.07956.0526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:50)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 51:85)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 86:129)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 130:141)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 142:159)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 1:7)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 8:17)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 18:32)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 33:45)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 46:56)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 57:75)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 76:82)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 83:90)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 91:98)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 99:117)

+
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