[English] 日本語
Yorodumi
- PDB-8zld: Crystal structure of PfHO from Plasmodium falciparum at 2.78 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zld
TitleCrystal structure of PfHO from Plasmodium falciparum at 2.78 A
ComponentsHeme oxygenase
KeywordsDNA BINDING PROTEIN / Plasmodium falciparum / apicoplast organelle / RNA transcription / apicoplast genome / divergent heme oxygenase
Function / homologyheme oxygenase (decyclizing) activity / Haem oxygenase-like, multi-helical / Heme oxygenase
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.78 Å
AuthorsCaaveiro, J.M.M. / Senoo, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Burroughs Wellcome Fund United States
Citation
Journal: Biorxiv / Year: 2024
Title: Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis.
Authors: Blackwell, A.M. / Jami-Alahmadi, Y. / Nasamu, A.S. / Kudo, S. / Senoo, A. / Slam, C. / Tsumoto, K. / Wohlschlegel, J.A. / Caaveiro, J.M.M. / Goldberg, D.E. / Sigala, P.A.
#1: Journal: Elife / Year: 2024
Title: Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis
Authors: Blackwell, A.M. / Jami-Alahmadi, Y. / Nasamu, A.S. / Kudo, S. / Senoo, A. / Slam, C. / Tsumoto, K. / Wohlschlegel, J.A. / Caaveiro, J.M. / Goldberg, D.E. / Sigala, P.A.
History
DepositionMay 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heme oxygenase
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2104
Polymers56,0182
Non-polymers1922
Water27015
1
A: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1052
Polymers28,0091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area10410 Å2
MethodPISA
2
B: Heme oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1052
Polymers28,0091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.910, 55.370, 162.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Heme oxygenase


Mass: 28009.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1011900 / Plasmid: pET21d / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IJS6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.4M (NH4)2SO4, 0.65M Li2SO4, 0.1M sodium citrate tribasic dihydrate, pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→55.4 Å / Num. obs: 13064 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Net I/σ(I): 11.2
Reflection shellResolution: 2.78→2.93 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1843 / CC1/2: 0.779 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLM7.2.2data reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.78→45.79 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 32.054 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 9.627 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26366 573 4.4 %RANDOM
Rwork0.2027 ---
obs0.20539 12443 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.301 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---4.12 Å20 Å2
3---4.47 Å2
Refinement stepCycle: 1 / Resolution: 2.78→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 10 15 3101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133164
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172893
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6314271
X-RAY DIFFRACTIONr_angle_other_deg1.3261.5726733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36124.096166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.79515588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.484158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02668
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_it2.2164.0851466
X-RAY DIFFRACTIONr_mcbond_other2.2154.0831465
X-RAY DIFFRACTIONr_mcangle_it3.5576.1181826
X-RAY DIFFRACTIONr_mcangle_other3.5576.1211827
X-RAY DIFFRACTIONr_scbond_it2.3944.3371698
X-RAY DIFFRACTIONr_scbond_other2.3674.3341691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9826.4012433
X-RAY DIFFRACTIONr_long_range_B_refined7.56975.73612913
X-RAY DIFFRACTIONr_long_range_B_other7.56775.73312910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5852 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.78→2.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 41 -
Rwork0.314 871 -
obs--98.7 %
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)
13.0509-1.13281.03533.1546-1.50665.0251-0.0168-0.12660.03640.05330.0235-0.2687-0.21620.3193-0.00670.2885-0.04740.07810.1017-0.04090.191659.107241.417546.2078
23.68541.9175-1.56923.86-1.23143.1622-0.04390.04210.2462-0.133-0.03820.3152-0.1782-0.10180.08210.02490.0299-0.030.2714-0.02530.048345.806620.340278.4079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 298
2X-RAY DIFFRACTION2B95 - 299

+
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