[English] 日本語
Yorodumi
- PDB-3oz2: Crystal structure of a geranylgeranyl bacteriochlorophyll reducta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oz2
TitleCrystal structure of a geranylgeranyl bacteriochlorophyll reductase-like (Ta0516) from Thermoplasma acidophilum at 1.60 A resolution
ComponentsDigeranylgeranylglycerophospholipid reductase
KeywordsFlavoprotein / oxidoreductase / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase [NAD(P)H] / membrane lipid biosynthetic process / glycerophospholipid metabolic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / geranylgeranyl reductase activity / phospholipid biosynthetic process / FAD binding / NAD binding / NADP binding / plasma membrane
Similarity search - Function
Digeranylgeranylglycerophospholipid reductase / Geranylgeranyl reductase family / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...Digeranylgeranylglycerophospholipid reductase / Geranylgeranyl reductase family / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-OZ2 / Digeranylgeranylglycerophospholipid reductase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids.
Authors: Xu, Q. / Eguchi, T. / Mathews, I.I. / Rife, C.L. / Chiu, H.J. / Farr, C.L. / Feuerhelm, J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / ...Authors: Xu, Q. / Eguchi, T. / Mathews, I.I. / Rife, C.L. / Chiu, H.J. / Farr, C.L. / Feuerhelm, J. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Weekes, D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionOct 27, 2010ID: 3CGV
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Digeranylgeranylglycerophospholipid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,38716
Polymers44,0301
Non-polymers2,35715
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.590, 70.670, 117.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Digeranylgeranylglycerophospholipid reductase / DGGGPL reductase / 2 / 3-di-O-geranylgeranylglyceryl phosphate reductase / Geranylgeranyl reductase / GGR


Mass: 44029.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0516 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: Q9HKS9, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor

-
Non-polymers , 5 types, 347 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-OZ2 / (2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate


Mass: 704.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H69O10P
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15.00% Glycerol, 8.50% iso-Propanol, 17.00% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97920,0.97862
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 1, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97921
30.978621
ReflectionResolution: 1.6→45.257 Å / Num. obs: 55071 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.479 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.640.4662.4144044009199.6
1.64-1.690.3723140783912199.5
1.69-1.740.3053.7137733820199.6
1.74-1.790.2524.5134853726199.7
1.79-1.850.2055.5131953623199.8
1.85-1.910.1557.1127083500199.9
1.91-1.980.1169.2123283382199.9
1.98-2.070.09611.2119963281199.9
2.07-2.160.07913.4114203126199.9
2.16-2.260.0715.2108872980199.8
2.26-2.390.06117.4104832862199.8
2.39-2.530.05419.199112709199.6
2.53-2.70.05120.693392554199.5
2.7-2.920.04623.186332368199.1
2.92-3.20.0425.680212200199.4
3.2-3.580.03528.172151984198.6
3.58-4.130.03330.163601765198.5
4.13-5.060.03230.753371500198
5.06-7.160.03929.541041180196.4
7.16-45.2570.03829.42120648189.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→45.257 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.679 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.074
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. FAD IS MODELED BASED ON DENSITY AND FUNCTION. 6. A BACTERIAL LIPID FOUND IN THE ACTIVE SITE WAS TENTATIVELY ASSIGNED AS A PHOSPHATIDYLGYLCEROL (OZ2) BASED ON DENSITY AND FUNCTION. THE DENSITY FOR THE HEAD GROUP AND LIPID TAILS ARE POORLY DEFINED. 7. ETHYLENE GLYCOL (EDO) AND GLYCEROL (GOL) WERE MODELED BASED ON CRYSTALLIZATION/CYRO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1706 2794 5.1 %RANDOM
Rwork0.153 ---
obs0.1539 55071 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.48 Å2 / Biso mean: 29.0611 Å2 / Biso min: 9.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 157 332 3493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223467
X-RAY DIFFRACTIONr_bond_other_d0.0010.022432
X-RAY DIFFRACTIONr_angle_refined_deg1.6082.0144717
X-RAY DIFFRACTIONr_angle_other_deg0.91135996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40624.519135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2315620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9881520
X-RAY DIFFRACTIONr_chiral_restr0.0940.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213826
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02657
X-RAY DIFFRACTIONr_mcbond_it1.49732096
X-RAY DIFFRACTIONr_mcbond_other0.4223861
X-RAY DIFFRACTIONr_mcangle_it2.51853394
X-RAY DIFFRACTIONr_scbond_it4.12181371
X-RAY DIFFRACTIONr_scangle_it6.476111288
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 201 -
Rwork0.263 3771 -
all-3972 -
obs--99.13 %
Refinement TLS params.Method: refined / Origin x: 13.7612 Å / Origin y: 50.0025 Å / Origin z: 25.9353 Å
111213212223313233
T0.0365 Å20.0052 Å2-0.0031 Å2-0.0253 Å20.0049 Å2--0.017 Å2
L0.7487 °2-0.1416 °20.2747 °2-0.5438 °2-0.3801 °2--0.8513 °2
S-0.0504 Å °-0.1026 Å °0.0454 Å °0.1346 Å °0.0207 Å °-0.0113 Å °-0.0587 Å °-0.0632 Å °0.0298 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 396
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION1A502

+
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