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- PDB-4hin: 2.4A Resolution Structure of Bovine Cytochrome b5 (S71L) -

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Basic information

Entry
Database: PDB / ID: 4hin
Title2.4A Resolution Structure of Bovine Cytochrome b5 (S71L)
ComponentsCytochrome b5
KeywordsELECTRON TRANSPORT / CYTOCHROME B5 / HEME
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial outer membrane / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / metal ion binding
Similarity search - Function
Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome 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 / Roll / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsLovell, S. / Battaile, K.P. / Parthasarathy, S. / Sun, N. / Terzyan, S. / Zhang, X. / Rivera, M. / Kuczera, K. / Benson, D.R.
CitationJournal: To be Published
Title: 2.4A Resolution Structure of Bovine Cytochrome b5 (S71L)
Authors: Parthasarathy, S. / Sun, N. / Lovell, S. / Battaile, K.P. / Terzyan, S. / Zhang, X. / Rivera, M. / Kuczera, K. / Benson, D.R.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b5
B: Cytochrome b5
C: Cytochrome b5
D: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,72612
Polymers38,0064
Non-polymers2,7208
Water64936
1
A: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1813
Polymers9,5011
Non-polymers6802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1813
Polymers9,5011
Non-polymers6802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1813
Polymers9,5011
Non-polymers6802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome b5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1813
Polymers9,5011
Non-polymers6802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.530, 92.709, 48.990
Angle α, β, γ (deg.)90.000, 113.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytochrome b5


Mass: 9501.460 Da / Num. of mol.: 4 / Mutation: S71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CYB5A, CYB5 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00171
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 20% (w/v) PEG 8000, 100 mM Tris, 200 mM MgCl2, 10 mM CuCl2, pH 8.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→92.71 Å / Num. all: 15234 / Num. obs: 15234 / % possible obs: 99.23 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.41 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.8759
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.4-2.533.510.662.37792222199.5
2.53-2.683.480.527277209099.13
2.68-2.873.320.376532196698.98
2.87-3.13.420.296315184699.62
3.1-3.393.540.195977168799.61
3.39-3.793.340.125148154399.61
3.79-4.383.410.074611135299.18
4.38-5.373.290.063790115299.25
5.37-7.593.340.06294087998.38
7.59-92.713.20.04159249897.12

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.57 Å46.35 Å
Translation2.57 Å46.35 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EHB

1ehb


Resolution: 2.4→46.35 Å / Cor.coef. Fo:Fc: 0.9172 / Cor.coef. Fo:Fc free: 0.8874 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.422 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 761 5 %RANDOM
Rwork0.2086 ---
obs0.2104 15213 99.19 %-
all-15213 --
Displacement parametersBiso max: 101 Å2 / Biso mean: 41.6801 Å2 / Biso min: 15.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.2211 Å20 Å2-4.5176 Å2
2---7.9199 Å20 Å2
3---9.141 Å2
Refine analyzeLuzzati coordinate error obs: 0.332 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 176 36 2812
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1201SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes445HARMONIC5
X-RAY DIFFRACTIONt_it2860HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion343SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3015SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2860HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3940HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion2.84
LS refinement shellResolution: 2.4→2.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2912 149 5.42 %
Rwork0.2293 2602 -
all0.2326 2751 -
obs--99.19 %

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