[English] 日本語
Yorodumi
- PDB-4opd: Constructing tailored isoprenoid products by structure-guided mod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4opd
TitleConstructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase.
ComponentsConserved Archaeal protein
KeywordsOXIDOREDUCTASE / Rossmann Fold / Archaeal Protein
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors / glycerophospholipid metabolic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / phospholipid biosynthetic process
Similarity search - Function
Geranylgeranyl reductase family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / GERANYLGERANYL DIPHOSPHATE / Digeranylgeranylglycerophospholipid reductase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsMcAndrew, R.P. / Kung, Y. / Xie, X. / Liu, C. / Pereira, J.H. / Keasling, J.D. / Adams, P.D.
CitationJournal: Structure / Year: 2014
Title: Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase.
Authors: Kung, Y. / McAndrew, R.P. / Xie, X. / Liu, C.C. / Pereira, J.H. / Adams, P.D. / Keasling, J.D.
History
DepositionFeb 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conserved Archaeal protein
B: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,93410
Polymers101,6562
Non-polymers4,2788
Water14,250791
1
A: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9675
Polymers50,8281
Non-polymers2,1394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved Archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9675
Polymers50,8281
Non-polymers2,1394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.079, 63.234, 65.102
Angle α, β, γ (deg.)120.98, 89.97, 88.55
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Conserved Archaeal protein


Mass: 50828.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: Saci_0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4JA33, EC: 1.3.1.83
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical
ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H36O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 7.5, 10% PEG 3350, 0.2 M L-proline, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. all: 78094 / Num. obs: 75985 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 2.6 % / Rsym value: 0.547 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
BOSdata collection
PHENIX(phenix.phaser: dev_1525)model building
PHENIX(phenix.refine: dev_1525)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXdev_1525phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→42.101 Å / SU ML: 0.18 / σ(F): 0.09 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 1925 2.68 %RANDOM
Rwork0.146 ---
obs0.146 71762 90.65 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→42.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7136 0 256 791 8183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077740
X-RAY DIFFRACTIONf_angle_d1.06410493
X-RAY DIFFRACTIONf_dihedral_angle_d16.293029
X-RAY DIFFRACTIONf_chiral_restr0.0431098
X-RAY DIFFRACTIONf_plane_restr0.0051350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.86980.31751500.22225262X-RAY DIFFRACTION69
1.8698-1.94460.23781800.1766441X-RAY DIFFRACTION84
1.9446-2.03310.21891870.15456893X-RAY DIFFRACTION89
2.0331-2.14030.19741850.14936952X-RAY DIFFRACTION91
2.1403-2.27440.22221990.14397165X-RAY DIFFRACTION92
2.2744-2.450.20491940.14847257X-RAY DIFFRACTION94
2.45-2.69650.20982030.15417269X-RAY DIFFRACTION95
2.6965-3.08660.18832010.15257446X-RAY DIFFRACTION96
3.0866-3.88830.1792090.13677548X-RAY DIFFRACTION98
3.8883-42.1010.14942170.12797604X-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)
11.4891-0.01780.91880.22510.16671.0477-0.13-0.02650.3046-0.0767-0.03690.1465-0.1515-0.1120.16350.13780.0327-0.03320.1278-0.020.1903-29.4693-29.451816.747
21.13550.21030.14181.20960.62650.90230.0022-0.0905-0.03640.0004-0.10070.17580.0547-0.1730.0820.0938-0.00310.00140.1278-0.0030.1061-32.8052-47.276419.4683
31.4536-0.32160.25183.2340.21332.0256-0.0643-0.24150.22590.2946-0.10760.1432-0.1474-0.04940.13750.1246-0.0088-0.01260.1784-0.05320.1436-14.9408-26.740634.3742
41.10130.40250.2260.95950.02530.3344-0.03860.01820.1053-0.12030.00920.082-0.0468-0.01430.03240.08640.0145-0.00480.09160.00050.0859-21.6097-39.258413.6977
52.07590.8233-0.2341.84641.16462.33990.04840.21550.3208-0.20130.1381-0.1516-0.25290.1481-0.16970.1520.00930.02190.22340.02370.233.1632-31.097921.3371
64.11311.94052.08122.98651.73242.906-0.04480.3446-0.5156-0.1740.1883-0.44860.13570.4411-0.11060.15360.02310.04170.2182-0.02880.2184-5.1952-47.958210.8908
71.68040.9429-0.3281.1446-0.14360.355-0.12220.2602-0.1913-0.19520.1318-0.2247-0.0090.0588-0.02060.1439-0.0090.04290.153-0.03640.169-35.7237-60.635136.111
82.3822-2.1919-0.72972.1750.91661.0803-0.081-0.25220.14880.17760.2664-0.5969-0.02120.2271-0.17110.1085-0.0092-0.01450.1554-0.02860.2601-23.8379-52.165754.5377
91.09780.71340.1681.34280.15130.6208-0.00310.0499-0.2507-0.02360.055-0.18390.09430.0244-0.04990.09020.00910.01050.09120.00260.1451-44.9728-65.8645.6302
102.86772.02960.16222.4550.34950.5451-0.10180.13690.0715-0.1540.06580.131-0.0983-0.05040.0410.1270.0313-0.01720.12060.01910.1043-53.2204-53.350141.8824
113.57922.070.08983.2189-0.31871.3534-0.20770.61490.1457-0.31870.02170.166-0.042-0.08440.20370.14750.0185-0.00160.29730.02050.3004-70.3178-59.998939.0544
125.01633.20810.6015.39481.07481.73470.0004-0.36940.52030.0471-0.09710.494-0.2045-0.24560.07890.14530.05370.00310.173-0.03090.1966-58.6856-45.503150.2109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:116 )A2 - 116
2X-RAY DIFFRACTION2( CHAIN A AND RESID 117:192 )A117 - 192
3X-RAY DIFFRACTION3( CHAIN A AND RESID 193:254 )A193 - 254
4X-RAY DIFFRACTION4( CHAIN A AND RESID 255:351 )A255 - 351
5X-RAY DIFFRACTION5( CHAIN A AND RESID 352:408 )A352 - 408
6X-RAY DIFFRACTION6( CHAIN A AND RESID 409:452 )A409 - 452
7X-RAY DIFFRACTION7( CHAIN B AND RESID 2:118 )B2 - 118
8X-RAY DIFFRACTION8( CHAIN B AND RESID 119:146 )B119 - 146
9X-RAY DIFFRACTION9( CHAIN B AND RESID 147:313 )B147 - 313
10X-RAY DIFFRACTION10( CHAIN B AND RESID 314:374 )B314 - 374
11X-RAY DIFFRACTION11( CHAIN B AND RESID 375:415 )B375 - 415
12X-RAY DIFFRACTION12( CHAIN B AND RESID 416:452 )B416 - 452

+
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