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- PDB-4o79: Crystal Structure of Ascorbate-bound Cytochrome b561, crystal soa... -

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Basic information

Entry
Database: PDB / ID: 4o79
TitleCrystal Structure of Ascorbate-bound Cytochrome b561, crystal soaked in 1 M L-ascorbate for 10 minutes
ComponentsProbable transmembrane ascorbate ferrireductase 2
KeywordsOXIDOREDUCTASE / alpha helical membrane protein / ascorbate-dependent oxidoreductase
Function / homology
Function and homology information


ferric-chelate reductase activity / ascorbate ferrireductase (transmembrane) / transmembrane ascorbate ferrireductase activity / L-ascorbic acid metabolic process / oxidoreductase activity / Golgi apparatus / integral component of membrane / metal ion binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1770 / Eukaryotic cytochrome b561 / Cytochrome b561/Cytochrome b reductase 1-like / Cytochrome b561/ferric reductase transmembrane / Cytochrome b561 domain profile. / Cytochrome b-561 / ferric reductase transmembrane domain. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ASCORBIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Transmembrane ascorbate ferrireductase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsLu, P. / Ma, D. / Yan, C. / Gong, X. / Du, M. / Shi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure and mechanism of a eukaryotic transmembrane ascorbate-dependent oxidoreductase
Authors: Lu, P. / Ma, D. / Yan, C. / Gong, X. / Du, M. / Shi, Y.
History
DepositionDec 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references / Non-polymer description
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transmembrane ascorbate ferrireductase 2
B: Probable transmembrane ascorbate ferrireductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3588
Polymers50,6202
Non-polymers2,7386
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-125 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.193, 108.648, 111.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Probable transmembrane ascorbate ferrireductase 2 / Cytochrome b561-1 / Artb561-2 / AtCytb561


Mass: 25310.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYB561B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SWS1, EC: 1.16.5.1
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG400, 400mM Li2SO4, 100 mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 30170 / Num. obs: 29506 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 33.72 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 87

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O6Y
Resolution: 2.003→30.585 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8514 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1499 5.08 %RANDOM
Rwork0.2017 ---
obs0.2023 29496 97.55 %-
all-30170 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 119.63 Å2 / Biso mean: 43.8759 Å2 / Biso min: 22.12 Å2
Baniso -1Baniso -2Baniso -3
1-6.178 Å20 Å2-0 Å2
2---9.7047 Å2-0 Å2
3---3.5267 Å2
Refinement stepCycle: LAST / Resolution: 2.003→30.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 189 66 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083600
X-RAY DIFFRACTIONf_angle_d1.1334958
X-RAY DIFFRACTIONf_chiral_restr0.063555
X-RAY DIFFRACTIONf_plane_restr0.004572
X-RAY DIFFRACTIONf_dihedral_angle_d14.941178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0031-2.06770.29541170.27742180229785
2.0677-2.14160.26981340.24532436257095
2.1416-2.22730.2641320.234425832715100
2.2273-2.32870.22921250.208625982723100
2.3287-2.45140.22351440.186725722716100
2.4514-2.60490.19281340.185525942728100
2.6049-2.80590.18081380.177525882726100
2.8059-3.0880.21851460.187925942740100
3.088-3.53430.21791430.188926062749100
3.5343-4.45070.19021520.18222607275999
4.4507-30.58810.21481340.22312639277395
Refinement TLS params.Method: refined / Origin x: 12.4521 Å / Origin y: 24.2453 Å / Origin z: -23.5938 Å
111213212223313233
T0.2454 Å2-0.021 Å20.0179 Å2-0.2878 Å20.044 Å2--0.2867 Å2
L1.1504 °2-0.3579 °20.297 °2-1.2073 °2-0.2294 °2--1.3191 °2
S0.0211 Å °0.0267 Å °-0.03 Å °0.0031 Å °-0.0377 Å °0.021 Å °0.0513 Å °0.0546 Å °0 Å °
Refinement TLS groupSelection details: ALL

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