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- PDB-9bl1: Crystal structure of heme-binding protein from Populus trichocarpa -

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Basic information

Entry
Database: PDB / ID: 9bl1
TitleCrystal structure of heme-binding protein from Populus trichocarpa
ComponentsHeme-binding protein, PtHOZ1
KeywordsMETAL BINDING PROTEIN / Heme binding protein / split-barrel family / SAD phasing
Function / homologyCREG, beta-barrel / Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / FMN-binding split barrel / NICKEL (II) ION / DUF2470 domain-containing protein
Function and homology information
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKumaran, D. / Grosjean, N. / Blaby, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)Quantitative Plant Science Initiative, SFA United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Functional diversification within the heme-binding split-barrel family.
Authors: Grosjean, N. / Zhang, L. / Kumaran, D. / Xie, M. / Fahey, A. / Santiago, K. / Hu, F. / Regulski, M. / Blaby, I.K. / Ware, D. / Blaby-Haas, C.E.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-binding protein, PtHOZ1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5593
Polymers32,4411
Non-polymers1172
Water1,74797
1
A: Heme-binding protein, PtHOZ1
hetero molecules

A: Heme-binding protein, PtHOZ1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1186
Polymers64,8832
Non-polymers2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3060 Å2
ΔGint-59 kcal/mol
Surface area26970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.306, 77.306, 92.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Heme-binding protein, PtHOZ1


Mass: 32441.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N7FVG6
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG monomethyl ether 2000, 10 mM nickel chloride and 100 mM sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 25732 / % possible obs: 96.7 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.061 / Χ2: 1.03 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2 / Num. unique obs: 1726 / CC1/2: 0.647 / CC star: 0.886 / % possible all: 79.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→38.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.212 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 1262 4.9 %RANDOM
Rwork0.20644 ---
obs0.20881 24413 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.387 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.7 Å20 Å2
3---1.39 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 2 97 2161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132107
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151989
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6472858
X-RAY DIFFRACTIONr_angle_other_deg1.341.5814591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3725263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07622.685108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52515341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9681512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02470
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_it4.0554.1961055
X-RAY DIFFRACTIONr_mcbond_other4.0484.1931054
X-RAY DIFFRACTIONr_mcangle_it6.1296.2771317
X-RAY DIFFRACTIONr_mcangle_other6.1316.2791318
X-RAY DIFFRACTIONr_scbond_it4.5794.7551051
X-RAY DIFFRACTIONr_scbond_other4.5774.7581052
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1436.9151542
X-RAY DIFFRACTIONr_long_range_B_refined10.43650.5012229
X-RAY DIFFRACTIONr_long_range_B_other10.43750.52222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 70 -
Rwork0.367 1429 -
obs--78.15 %

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