[English] 日本語
Yorodumi
- PDB-6r46: Crystal structure of LPOR (Thermosynechococcus elongatus) complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r46
TitleCrystal structure of LPOR (Thermosynechococcus elongatus) complexed with NADP+ at 2.5A resolution
ComponentsNADPH-protochlorophyllide oxidoreductase
KeywordsHYDROLASE / complex
Function / homology
Function and homology information


protochlorophyllide reductase / protochlorophyllide reductase activity / chlorophyll biosynthetic process / photosynthesis / nucleotide binding / metal ion binding
Similarity search - Function
Light-dependent protochlorophyllide reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / protochlorophyllide reductase
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhou, A. / Feng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Nature / Year: 2019
Title: Structural basis for enzymatic photocatalysis in chlorophyll biosynthesis.
Authors: Zhang, S. / Heyes, D.J. / Feng, L. / Sun, W. / Johannissen, L.O. / Liu, H. / Levy, C.W. / Li, X. / Yang, J. / Yu, X. / Lin, M. / Hardman, S.J.O. / Hoeven, R. / Sakuma, M. / Hay, S. / Leys, D. ...Authors: Zhang, S. / Heyes, D.J. / Feng, L. / Sun, W. / Johannissen, L.O. / Liu, H. / Levy, C.W. / Li, X. / Yang, J. / Yu, X. / Lin, M. / Hardman, S.J.O. / Hoeven, R. / Sakuma, M. / Hay, S. / Leys, D. / Rao, Z. / Zhou, A. / Cheng, Q. / Scrutton, N.S.
History
DepositionMar 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH-protochlorophyllide oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,02511
Polymers35,8121
Non-polymers1,21210
Water36020
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-156 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.950, 134.950, 104.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-407-

CL

21A-409-

CL

31A-520-

HOH

-
Components

#1: Protein NADPH-protochlorophyllide oxidoreductase


Mass: 35812.340 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Gene: por / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DLC1, protochlorophyllide reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 10MM ZNSO4,0.2M LI3CITRATE, 30% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.5→78 Å / Num. obs: 20005 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 20005 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0189refinement
RefinementMethod to determine structure: SAD / Resolution: 2.5→78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.784 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.216 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 976 4.9 %RANDOM
Rwork0.196 ---
obs0.198 19000 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 57 20 2217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192236
X-RAY DIFFRACTIONr_bond_other_d0.0020.022104
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9923032
X-RAY DIFFRACTIONr_angle_other_deg1.00134871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21223.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6315375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8151515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
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_it2.3575.1941096
X-RAY DIFFRACTIONr_mcbond_other2.3485.1921095
X-RAY DIFFRACTIONr_mcangle_it3.7487.7661363
X-RAY DIFFRACTIONr_mcangle_other3.7487.7671364
X-RAY DIFFRACTIONr_scbond_it2.9125.8491140
X-RAY DIFFRACTIONr_scbond_other2.9115.8571141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7788.7141670
X-RAY DIFFRACTIONr_long_range_B_refined8.30761.5132412
X-RAY DIFFRACTIONr_long_range_B_other8.30861.532412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 66 -
Rwork0.288 1358 -
obs--99.23 %
Refinement TLS params.Method: refined / Origin x: -40.8526 Å / Origin y: -33.9259 Å / Origin z: -9.5193 Å
111213212223313233
T0.1973 Å2-0.0375 Å2-0.0155 Å2-0.1759 Å20.0717 Å2--0.0654 Å2
L0.3868 °20.2329 °20.3143 °2-0.9418 °2-0.0484 °2--0.8905 °2
S-0.1127 Å °0.0942 Å °0.1173 Å °0.2315 Å °-0.1068 Å °0.0185 Å °-0.0206 Å °0.1758 Å °0.2195 Å °

+
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