[English] 日本語
Yorodumi
- PDB-1vju: Coproporphyrinogen III oxidase from Leishmania major -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vju
TitleCoproporphyrinogen III oxidase from Leishmania major
ComponentsCoproporphyrinogen III oxidase
KeywordsOXIDOREDUCTASE / structural genomics / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


coproporphyrinogen oxidase / coproporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / chloroplast stroma / protein homodimerization activity / cytoplasm
Similarity search - Function
Coproporphyrinogen III oxidase, aerobic / Coproporphyrinogen III oxidase, aerobic / Coproporphyrinogen III oxidase, conserved site / Oxygen-dependent coproporphyrinogen III oxidase superfamily / Coproporphyrinogen III oxidase / Coproporphyrinogen III oxidase signature. / oxygen-dependent coproporphyrinogen oxidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxygen-dependent coproporphyrinogen-III oxidase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.401 Å
AuthorsStructural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Coproporphyrinogen III oxidase from Leishmania major
Authors: Structural Genomics of Pathogenic Protozoa Consortium
History
DepositionMar 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Dec 27, 2023Group: 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 / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE THERE WAS NO SUITABLE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN AT THE TIME OF ...SEQUENCE THERE WAS NO SUITABLE SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THIS TARGET ORF DOES NOT YET HAVE A SEQUENCE ID IN GENEDB; ITS PROVISIONAL LISTING CODE IS CHR6_TMP.82

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coproporphyrinogen III oxidase
B: Coproporphyrinogen III oxidase


Theoretical massNumber of molelcules
Total (without water)71,4462
Polymers71,4462
Non-polymers00
Water11,602644
1
A: Coproporphyrinogen III oxidase


Theoretical massNumber of molelcules
Total (without water)35,7231
Polymers35,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coproporphyrinogen III oxidase


Theoretical massNumber of molelcules
Total (without water)35,7231
Polymers35,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.649, 53.734, 66.627
Angle α, β, γ (deg.)86.456, 77.126, 61.501
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Coproporphyrinogen III oxidase


Mass: 35723.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid details: SGPP target construct Lmaj006828AAA / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P84155, coproporphyrinogen oxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4 ul protein 19 mg/ml, 0.4 ul crystallization buffer: 29% PEG 5000MME, 200 mM Ammonium sulfate, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97954
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.401→64.55 Å / Num. all: 238100 / Num. obs: 116623 / % possible obs: 95.1 % / Redundancy: 3.85 % / Limit h max: 37 / Limit h min: -37 / Limit k max: 38 / Limit k min: -38 / Limit l max: 47 / Limit l min: -47 / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.64
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 92.9

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 1.8 Å / D res low: 50 Å / FOM : 0.62 / Reflection: 56354
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1110.97957.41-4.12
1120.97973.58-14.8
1130.97875.29-7.5
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
137.74444.4029.289S201
223.93222.994-7.912S200.924
339.69520.37516.615S200.854
416.63531.2140.09S200.754
526.09846.9490.005S200.698
647.09528.769.215S200.571
740.58652.9287.028S200.38
823.22156.3541.998S200.35
96.21711.9-20.816S200.235
10-4.0290.128-16.016S200.115
1145.76234.49417.181S200.052
Phasing MAD shell
Resolution (Å)FOM Reflection
6.54-500.72558
4.11-6.540.624621
3.2-4.110.665994
2.71-3.20.697022
2.4-2.710.677966
2.17-2.40.648714
2-2.170.599453
1.86-20.5210026
Phasing dmFOM : 0.83 / FOM acentric: 0.83 / FOM centric: 0 / Reflection: 56354 / Reflection acentric: 56354 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.1-41.5410.960.960243724370
3.2-5.10.960.960761776170
2.6-3.20.920.920953195310
2.3-2.60.870.870955195510
1.9-2.30.80.8016890168900
1.8-1.90.650.65010328103280

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
SHELXphasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0000 24/04/2001refinement
SHELXDphasing
RefinementResolution: 1.401→40 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.806 / SU ML: 0.033 / ESU R: 0.054 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1804 5858 5.023 %
Rwork0.1514 --
obs-116622 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 15.325 Å2
Baniso -1Baniso -2Baniso -3
1-0.007 Å2-0.287 Å20.281 Å2
2--0.314 Å2-0.06 Å2
3----0.165 Å2
Refinement stepCycle: LAST / Resolution: 1.401→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 0 644 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224829
X-RAY DIFFRACTIONr_bond_other_d0.0010.024217
X-RAY DIFFRACTIONr_angle_refined_deg2.5221.9186541
X-RAY DIFFRACTIONr_angle_other_deg1.07739756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12423.216255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56315746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8441540
X-RAY DIFFRACTIONr_chiral_restr0.1490.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025512
X-RAY DIFFRACTIONr_gen_planes_other00.021120
X-RAY DIFFRACTIONr_nbd_refined0.2330.21000
X-RAY DIFFRACTIONr_nbd_other0.2130.24186
X-RAY DIFFRACTIONr_nbtor_refined0.2080.22388
X-RAY DIFFRACTIONr_nbtor_other0.10.22734
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2411
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4350.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.243
X-RAY DIFFRACTIONr_mcbond_it2.83623053
X-RAY DIFFRACTIONr_mcbond_other0.6721208
X-RAY DIFFRACTIONr_mcangle_it3.49134630
X-RAY DIFFRACTIONr_mcangle_other2.07233991
X-RAY DIFFRACTIONr_scbond_it3.74722183
X-RAY DIFFRACTIONr_scbond_other1.28824079
X-RAY DIFFRACTIONr_scangle_it5.33331911
X-RAY DIFFRACTIONr_scangle_other2.68935765
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.401-1.43710.254320.22477399040
1.437-1.47640.244280.278438854
1.476-1.51910.2033960.17777088631
1.519-1.56580.2113940.16475128362
1.566-1.61710.2033820.1572978104
1.617-1.67370.1893960.14970447841
1.674-1.73680.1673470.14468587559
1.737-1.80760.1623280.14266647306
1.808-1.88780.1873300.14163546959
1.888-1.97970.1723570.13960696672
1.98-2.08650.1532990.13558416364
2.087-2.21270.1532950.13354925984
2.213-2.3650.1572450.13252665688
2.365-2.55370.1652730.13947765218
2.554-2.79630.1872380.14744144833
2.796-3.12450.1811980.15540114383
3.124-3.60410.2011780.14735003872
3.604-4.40520.1541570.14629153261
4.405-6.19250.1931230.17522342511
6.192-400.224620.22512271421

+
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