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- PDB-6nzx: Hadesarchaea YNP_N21 cytochrome b5 domain protein (KUO41884.1) -

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Basic information

Entry
Database: PDB / ID: 6nzx
TitleHadesarchaea YNP_N21 cytochrome b5 domain protein (KUO41884.1)
ComponentsCytochrome B5
KeywordsMETAL BINDING PROTEIN / Cytochrome B5 / metal-binding / heme-binding / electron transport / transport / HEME BINDING PROTEIN
Function / homologyCytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome B5
Function and homology information
Biological speciesHadesarchaea archaeon YNP_N21 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTeakel, S.L. / Marama, M.S. / Aragao, D. / Forwood, J.K. / Cahill, M.A.
CitationJournal: To Be Published
Title: Hadesarchaea YNP_N21 cytochrome b5 domain protein (KUO41884.1)
Authors: Teakel, S.L. / Marama, M.S. / Aragao, D. / Forwood, J.K. / Cahill, M.A.
History
DepositionFeb 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2432
Polymers8,6271
Non-polymers6161
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.170, 72.170, 22.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Cytochrome B5


Mass: 8626.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hadesarchaea archaeon YNP_N21 (archaea)
Gene: APU95_03975 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A147JZ41
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M sodium citrate, 2M ammonium sulfate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→23.62 Å / Num. obs: 5554 / % possible obs: 100 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.04 / Rrim(I) all: 0.183 / Χ2: 0.94 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 20.8 % / Rmerge(I) obs: 2.1 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 363 / Rpim(I) all: 0.47 / Rrim(I) all: 2.152 / Χ2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J03

1j03


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.359 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26067 280 5.1 %RANDOM
Rwork0.2206 ---
obs0.22266 5262 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0.44 Å20 Å2
2---0.87 Å20 Å2
3---2.83 Å2
Refinement stepCycle: 1 / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms599 0 43 21 663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.015668
X-RAY DIFFRACTIONr_bond_other_d0.0020.017584
X-RAY DIFFRACTIONr_angle_refined_deg2.351.775912
X-RAY DIFFRACTIONr_angle_other_deg0.8851.7141356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.955575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.71121.21233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83515100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.84154
X-RAY DIFFRACTIONr_chiral_restr0.0580.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02760
X-RAY DIFFRACTIONr_gen_planes_other0.010.02142
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_it2.2142.709303
X-RAY DIFFRACTIONr_mcbond_other2.1142.701302
X-RAY DIFFRACTIONr_mcangle_it3.4714.05377
X-RAY DIFFRACTIONr_mcangle_other3.4814.054378
X-RAY DIFFRACTIONr_scbond_it2.6213.065365
X-RAY DIFFRACTIONr_scbond_other2.5653.048363
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1324.444536
X-RAY DIFFRACTIONr_long_range_B_refined5.83231.198771
X-RAY DIFFRACTIONr_long_range_B_other5.8931.2768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 16 -
Rwork0.372 375 -
obs--100 %

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