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- PDB-4hil: 1.25A Resolution Structure of Rat Type B Cytochrome b5 -

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Basic information

Entry
Database: PDB / ID: 4hil
Title1.25A Resolution Structure of Rat Type B Cytochrome b5
ComponentsCytochrome b5 type B
KeywordsELECTRON TRANSPORT / CYTOCHROME B5 / HEME
Function / homology
Function and homology information


Sphingolipid de novo biosynthesis / Phase I - Functionalization of compounds / nitric-oxide synthase complex / nitrite reductase (NO-forming) activity / ubiquinol-cytochrome-c reductase activity / enzyme activator activity / nitric oxide biosynthetic process / mitochondrial outer membrane / intracellular membrane-bounded organelle / heme binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5 type B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 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: 1.25A Resolution Structure of Rat Type B Cytochrome b5
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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 type B
B: Cytochrome b5 type B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0345
Polymers19,7782
Non-polymers1,2563
Water4,197233
1
A: Cytochrome b5 type B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5052
Polymers9,8891
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome b5 type B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5283
Polymers9,8891
Non-polymers6392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.609, 67.847, 70.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome b5 type B / Cytochrome b5 outer mitochondrial membrane isoform


Mass: 9888.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cyb5b, Cyb5m, Omb5 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04166
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 30% (w/v) PEG 8000, 100 sodium cacodylate, 200 mM sodium acetate, pH 6.5, 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: Jun 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→48.833 Å / Num. all: 51942 / Num. obs: 51942 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rsym value: 0.066 / Net I/σ(I): 13.4
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 7483 / Rsym value: 0.757 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.56 Å35.17 Å
Translation1.56 Å35.17 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
PHENIX1.7.3_927refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MUS

3mus


Resolution: 1.25→35.171 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1522 2643 5.1 %RANDOM
Rwork0.1371 ---
obs0.1379 51871 99.95 %-
all-51871 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.497 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 46.74 Å2 / Biso mean: 15.8343 Å2 / Biso min: 5.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.9117 Å2-0 Å20 Å2
2---5.0101 Å20 Å2
3---4.0984 Å2
Refinement stepCycle: LAST / Resolution: 1.25→35.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 87 233 1648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111588
X-RAY DIFFRACTIONf_angle_d1.3282217
X-RAY DIFFRACTIONf_chiral_restr0.071201
X-RAY DIFFRACTIONf_plane_restr0.009274
X-RAY DIFFRACTIONf_dihedral_angle_d17.86550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.25-1.27270.26551460.234725252671
1.2727-1.29720.23941580.205625552713
1.2972-1.32370.19671300.183925682698
1.3237-1.35250.15981220.160425562678
1.3525-1.38390.15051470.138725772724
1.3839-1.41850.18961420.123625212663
1.4185-1.45690.16221420.124425582700
1.4569-1.49980.13881370.106426022739
1.4998-1.54820.1261170.105125702687
1.5482-1.60350.13991230.109625892712
1.6035-1.66770.14841360.104725702706
1.6677-1.74360.13091570.103925802737
1.7436-1.83550.1341510.108225692720
1.8355-1.95050.12721290.113326022731
1.9505-2.10110.14031570.12125692726
2.1011-2.31250.13751350.125426212756
2.3125-2.64710.14811430.138426272770
2.6471-3.33460.17831370.157426642801
3.3346-35.18490.14531340.154928052939

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