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- PDB-5hav: Sperm whale myoglobin mutant L29H F33Y F43H (F33Y CuBMb) with oxy... -

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Basic information

Entry
Database: PDB / ID: 5hav
TitleSperm whale myoglobin mutant L29H F33Y F43H (F33Y CuBMb) with oxygen bound
ComponentsMyoglobin
KeywordsOXIDOREDUCTASE / oxidase
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.268 Å
AuthorsPetrik, I.D. / 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: 2016
Title: Spectroscopic and Crystallographic Evidence for the Role of a Water-Containing H-Bond Network in Oxidase Activity of an Engineered Myoglobin.
Authors: Petrik, I.D. / Davydov, R. / Ross, M. / Zhao, X. / Hoffman, B. / Lu, Y.
History
DepositionDec 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 17, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)17,9153
Polymers17,2671
Non-polymers6482
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.632, 47.609, 76.534
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: 17266.914 Da / Num. of mol.: 1 / Mutation: L29H F33Y F43H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pT-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Crystallization solution: 30% PEG 10000, 200 mM sodium acetate, 100 mM sodium MES ph 6.75 Protein solution: 1 mM protein, 20 mM Tris sulfate ph 8.0, Solutions mixed 1:1 at 200uL final volume ...Details: Crystallization solution: 30% PEG 10000, 200 mM sodium acetate, 100 mM sodium MES ph 6.75 Protein solution: 1 mM protein, 20 mM Tris sulfate ph 8.0, Solutions mixed 1:1 at 200uL final volume and equilibrated by sitting drop vapor diffusion against 30 mL of crystallization solution in the dark
PH range: 6.7-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.268→50 Å / Num. obs: 39055 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.98 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Χ2: 1.388 / Net I/av σ(I): 43.591 / Net I/σ(I): 17.9 / Num. measured all: 171512
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.268-1.292.60.32918530.8560.2290.4041.02594.8
1.29-1.323.10.30618940.8930.1990.3681.10399
1.32-1.343.80.29519100.9120.1720.3441.151100
1.34-1.374.60.26519770.9470.1390.31.19100
1.37-1.44.60.23718900.9560.1240.2681.18299.9
1.4-1.434.60.20219300.9670.1060.2291.219100
1.43-1.474.60.16319370.9770.0850.1851.208100
1.47-1.514.60.12519260.9880.0650.1411.24399.9
1.51-1.554.70.10819410.990.0570.1231.234100
1.55-1.64.60.09219510.9920.0480.1041.234100
1.6-1.664.70.0819380.9940.0410.091.292100
1.66-1.724.70.06419650.9960.0330.0721.232100
1.72-1.84.70.05719370.9950.0290.0641.287100
1.8-1.94.70.04219520.9980.0220.0481.218100
1.9-2.024.60.03419550.9990.0170.0381.20199.9
2.02-2.174.60.03319700.9990.0170.0371.48199.9
2.17-2.394.60.03819850.9980.020.0432.183100
2.39-2.744.60.03619910.9980.0180.042.23899.8
2.74-3.454.40.02520290.9990.0130.0281.435100
3.45-504.20.03221240.9970.0170.0372.01799.3

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Processing

Software
NameVersionClassification
PHENIXphenix.refine: 1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4FWX

4fwx


Resolution: 1.268→23.832 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3471 4.76 %previous model flags + random
Rwork0.146 69479 --
obs0.1476 72950 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.8 Å2 / Biso mean: 18.2429 Å2 / Biso min: 9.71 Å2
Refinement stepCycle: final / Resolution: 1.268→23.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 45 243 1507
Biso mean--12.95 28 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171368
X-RAY DIFFRACTIONf_angle_d2.0971856
X-RAY DIFFRACTIONf_chiral_restr0.076194
X-RAY DIFFRACTIONf_plane_restr0.011228
X-RAY DIFFRACTIONf_dihedral_angle_d18.641521
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 (%)
1.2681-1.28550.22881180.22182356247482
1.2855-1.30380.26561280.21482546267492
1.3038-1.32330.24591420.1992786292896
1.3233-1.3440.26411330.18932739287299
1.344-1.3660.21431470.17328803027100
1.366-1.38960.21081350.170127362871100
1.3896-1.41480.23531390.15728623001100
1.4148-1.4420.20921430.15328032946100
1.442-1.47150.17441390.135728492988100
1.4715-1.50350.18761340.12362761289599
1.5035-1.53840.17051440.128528633007100
1.5384-1.57690.16761400.120727702910100
1.5769-1.61950.18751410.123328372978100
1.6195-1.66720.15251490.12172829297899
1.6672-1.7210.17271470.129428192966100
1.721-1.78240.16471320.133627712903100
1.7824-1.85380.17261380.140728192957100
1.8538-1.93810.15491340.13412843297799
1.9381-2.04020.16751610.141327742935100
2.0402-2.1680.15511330.13672822295599
2.168-2.33530.19171310.14342817294899
2.3353-2.570.15971550.14952797295299
2.57-2.94130.1881220.15732808293099
2.9413-3.70350.15861340.14522794292899
3.7035-23.83580.18351520.14942798295099

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