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- PDB-4tyx: Structure of aquoferric sperm whale myoglobin L29H/F33Y/F43H/S92A... -

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Basic information

Entry
Database: PDB / ID: 4tyx
TitleStructure of aquoferric sperm whale myoglobin L29H/F33Y/F43H/S92A mutant
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / OXIDOREDUCTASE / Globin / Artificial / Engineered
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsBhagi-Damodaran, A. / Petrik, I.D. / Robinson, H. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM062211 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Systematic tuning of heme redox potentials and its effects on O2 reduction rates in a designed oxidase in myoglobin.
Authors: Bhagi-Damodaran, A. / Petrik, I.D. / Marshall, N.M. / Robinson, H. / Lu, Y.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8672
Polymers17,2511
Non-polymers6161
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.467, 47.910, 76.854
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 Myoglobin /


Mass: 17250.914 Da / Num. of mol.: 1 / Mutation: S92A,F33Y,L29H,F43H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 0.1M NaMES pH 6.57, 0.02M Tris sulfate pH 8, 0.2M NaOAc, 30% PEG 6K
PH range: 6.57

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 18486 / % possible obs: 99.3 % / Redundancy: 15.1 % / Biso Wilson estimate: 21.06 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.331 / Net I/av σ(I): 31.76 / Net I/σ(I): 13.2 / Num. measured all: 278363
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.64-1.713.30.46216821.06192.9
1.7-1.7714.20.3818231.174100
1.77-1.8514.20.29918441.264100
1.85-1.9414.20.22918141.523100
1.94-2.0714.20.1818501.647100
2.07-2.2314.20.14118331.686100
2.23-2.4514.20.11518601.524100
2.45-2.814.10.09218771.299100
2.8-3.5318.20.09918841.119100
3.53-5019.30.08220191.142100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CBASSdata collection
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FWX

4fwx


Resolution: 1.64→40.657 Å / FOM work R set: 0.8791 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1975 3447 10.02 %
Rwork0.1563 30956 -
obs0.1604 34403 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.26 Å2 / Biso mean: 25.23 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 1.64→40.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 43 178 1439
Biso mean--22.46 33.84 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171323
X-RAY DIFFRACTIONf_angle_d1.7841800
X-RAY DIFFRACTIONf_chiral_restr0.339187
X-RAY DIFFRACTIONf_plane_restr0.008221
X-RAY DIFFRACTIONf_dihedral_angle_d20.58495
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.66250.26021240.18291133125794
1.6625-1.68620.23011370.172612411378100
1.6862-1.71140.2081440.17612851429100
1.7114-1.73810.23161300.172512241354100
1.7381-1.76660.22711400.176312551395100
1.7666-1.79710.26671400.196412401380100
1.7971-1.82980.23131360.184212431379100
1.8298-1.8650.23751380.178612351373100
1.865-1.9030.23271370.176412231360100
1.903-1.94440.22171380.178912391377100
1.9444-1.98960.2421430.167112631406100
1.9896-2.03940.24231330.169512461379100
2.0394-2.09450.19551350.165112321367100
2.0945-2.15620.21961420.154512471389100
2.1562-2.22580.20121360.151312301366100
2.2258-2.30530.20371400.165612771417100
2.3053-2.39760.22981360.156612401376100
2.3976-2.50670.17591390.15812221361100
2.5067-2.63880.18161370.160512351372100
2.6388-2.80410.24561450.170612681413100
2.8041-3.02060.24451370.173412141351100
3.0206-3.32440.18641410.15912451386100
3.3244-3.80520.1611370.13912351372100
3.8052-4.79290.16371380.124412591397100
4.7929-40.66950.15491440.145312251369100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.728-0.29840.15180.21-0.32460.2081-0.04470.07610.08690.04550.03710.0960.025-0.02670.00020.1452-0.00370.01620.14530.0010.1298-5.1373-0.30570.2703
20.38150.1027-0.23420.1843-0.00860.2182-0.0070.1696-0.1268-0.1922-0.2354-0.2425-0.15490.573-0.39950.2090.06610.00680.5350.13430.13631.0782-3.6935-19.9478
30.0280.01240.00490.0229-0.01660.03050.22320.3794-0.1685-0.014-0.1648-0.09560.00230.07-0.00020.20740.04730.00680.2642-0.03930.162-10.0653-5.9764-18.0468
40.5355-0.13880.07390.7873-0.34870.1457-0.09930.08660.0033-0.02250.0194-0.15030.07230.094900.1497-0.0010.00330.1447-0.00650.14536.1468-6.9544-2.5833
50.3616-0.06840.2560.09080.13610.18270.00640.23620.2862-0.0208-0.03130.0038-0.0931-0.0654-0.00270.1354-0.0078-0.00680.120.02950.1727-3.74884.9865-4.444
60.28160.02660.08650.0930.05520.2976-0.06360.10530.25910.07140.0293-0.0881-0.12590.0968-0.0320.15460.0037-0.01590.12960.00570.17929.00584.14490.1493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 51 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 58 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 100 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 124 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 153 )A0

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