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- PDB-7kyr: Crystal structure of I107E CuB myoglobin (I107E L29H F43H sperm w... -

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Basic information

Entry
Database: PDB / ID: 7kyr
TitleCrystal structure of I107E CuB myoglobin (I107E L29H F43H sperm whale myoglobin)
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / globin / oxidase / oxygen binding / oxygen reduction / OXIDOREDUCTASE
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsPetrik, I. / Lu, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM062211 United States
CitationJournal: Biochemistry / Year: 2021
Title: An Engineered Glutamate in Biosynthetic Models of Heme-Copper Oxidases Drives Complete Product Selectivity by Tuning the Hydrogen-Bonding Network.
Authors: Petrik, I.D. / Davydov, R. / Kahle, M. / Sandoval, B. / Dwaraknath, S. / Adelroth, P. / Hoffman, B. / Lu, Y.
History
DepositionDec 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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)18,3906
Polymers17,3981
Non-polymers9925
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.016, 31.728, 71.283
Angle α, β, γ (deg.)90.000, 102.353, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17398.066 Da / Num. of mol.: 1 / Mutation: L29H, F43H, I107E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02185

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Non-polymers , 6 types, 132 molecules

#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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.05 % / Description: Solid rectangular prism
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 1.5-2.0 mM protein in 20 mM tris sulfate pH 8.0 buffer, mixed 1:1 with crystallization solution composed of 100 mM tris sulfate pH 8.6, 200 mM sodium acetate, and 30% w/v PEG 10000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 16343 / % possible obs: 99.8 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.025 / Rrim(I) all: 0.077 / Χ2: 1.046 / Net I/σ(I): 11.5 / Num. measured all: 124786
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.765.80.63516000.8430.2850.6980.7598.5
1.76-1.836.60.48815960.9260.2040.5290.822100
1.83-1.916.90.32716290.9580.1330.3530.91899.9
1.91-2.027.10.22116320.9790.0880.2381.046100
2.02-2.147.30.15116040.9910.060.1631.141100
2.14-2.317.30.11116480.9940.0440.121.204100
2.31-2.547.30.08416210.9960.0330.091.154100
2.54-2.917.30.06716460.9970.0270.0721.147100
2.91-3.6610.20.08116490.9990.0260.0851.082100
3.66-5010.40.05417180.9990.0180.0571.062100

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Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070refinement
HKL-20002.3.8data scaling
PDB_EXTRACT3.25data extraction
HKL-20002.3.8data reduction
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FWZ

4fwz


Resolution: 1.71→34.83 Å / SU ML: 0.1868 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.4452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2098 3144 10.03 %
Rwork0.1662 28215 -
obs0.1706 31359 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.61 Å2
Refinement stepCycle: LAST / Resolution: 1.71→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 66 127 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451341
X-RAY DIFFRACTIONf_angle_d0.77211824
X-RAY DIFFRACTIONf_chiral_restr0.0417187
X-RAY DIFFRACTIONf_plane_restr0.0038223
X-RAY DIFFRACTIONf_dihedral_angle_d29.6224193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.33131270.27091044X-RAY DIFFRACTION83.29
1.73-1.760.29251580.28511278X-RAY DIFFRACTION97.75
1.76-1.790.30411400.25611318X-RAY DIFFRACTION99.66
1.79-1.830.26951440.24591260X-RAY DIFFRACTION99.57
1.83-1.860.27281600.21341329X-RAY DIFFRACTION100
1.86-1.90.24771290.21381283X-RAY DIFFRACTION99.93
1.9-1.940.23711250.22531320X-RAY DIFFRACTION99.93
1.94-1.990.23361600.1931292X-RAY DIFFRACTION100
1.99-2.040.24231340.17641275X-RAY DIFFRACTION100
2.04-2.090.18981430.16911302X-RAY DIFFRACTION100
2.09-2.150.20581310.16911268X-RAY DIFFRACTION99.86
2.15-2.220.20681420.16971335X-RAY DIFFRACTION100
2.22-2.30.21011440.16911278X-RAY DIFFRACTION99.93
2.3-2.390.21941420.171285X-RAY DIFFRACTION100
2.39-2.50.17611440.15691284X-RAY DIFFRACTION100
2.5-2.630.24971560.1651298X-RAY DIFFRACTION100
2.63-2.80.21571390.16941296X-RAY DIFFRACTION100
2.8-3.010.20741480.16921293X-RAY DIFFRACTION100
3.01-3.320.1951520.16441306X-RAY DIFFRACTION99.93
3.32-3.80.20481380.1381279X-RAY DIFFRACTION100
3.8-4.780.20551490.13261294X-RAY DIFFRACTION99.65
4.78-34.830.16351390.16291298X-RAY DIFFRACTION100
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)
12.55375733953-1.323158754550.2071687878763.13438974339-1.475350845183.9584639795-0.101060897872-0.151217649374-0.03003816554370.4455190011670.103999724220.125782635752-0.226456439777-0.0122815978958-0.0004489161883260.215200018304-0.0366427801539-0.0132865165070.149109193403-0.03908906402570.1582656069677.580542959162.2173345356823.8767108654
28.87339313991.39241726246-1.011263354144.68364918828-1.350876605371.53082829472-0.02332494402040.3081531705760.320838443643-0.3658224559550.04181103790990.436640965023-0.247888576047-0.132138655142-0.03462817698350.3082307164970.0232066866972-0.08027084714170.2559640586390.03048326540560.2557352590950.461680567849.71522366026.31465757678
33.14822242724-1.372219499050.9138551867233.87189131614-0.5493259021132.70541304092-0.03510037980210.0595985742086-0.196830957253-0.01070384896810.06444860569980.1605841086960.1612148269850.0203476754788-0.03800425446580.190531365927-0.0477362258453-0.01192539131760.134613455935-0.006801111544690.1873148260187.81734517752-5.6879024547313.3048496769
45.13891407695-1.76483994229-4.288918924554.269850660882.204356637743.877533807760.0933601635107-0.03440780657410.1201812156360.277550532934-0.00930874248494-0.145013755558-0.413961534654-0.0429625735954-0.1299743985980.194829312682-0.00836749987657-0.02041907405680.1280633298390.005134595229350.17002482010510.91427650417.6702598390920.5589924914
54.24935572951-0.3107030649881.185238073854.001367113690.3742381237365.548163591080.0620520504550.376361381176-0.268209321728-0.124610374991-0.00101033733259-0.1402318247780.1505083603130.31477767722-0.02271114529140.1578714188568.72757024767E-50.0276726019420.1285497205060.01856906336470.20656739778815.2800497259-2.5975023699413.8259983656
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 35 )A1 - 351 - 35
22chain 'A' and (resid 36 through 58 )A36 - 5836 - 58
33chain 'A' and (resid 59 through 100 )A59 - 10059 - 100
44chain 'A' and (resid 101 through 124 )A101 - 124101 - 124
55chain 'A' and (resid 125 through 152 )A - F125 - 152125

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