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- PDB-8zld: Crystal structure of PfHO from Plasmodium falciparum at 2.78 A -

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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: 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. / Manuel Martinez Caaveiro, J. / Goldberg, D.E. / Sigala, P.A.
#1: 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.
#2: 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
Revision 1.2Oct 8, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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