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- PDB-7l3u: Crystal structure of I107E F33Y CuB myoglobin (I107E F33Y L29H F4... -

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Basic information

Entry
Database: PDB / ID: 7l3u
TitleCrystal structure of I107E F33Y CuB myoglobin (I107E F33Y 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 macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 18, 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)18,0312
Polymers17,4141
Non-polymers6161
Water2,612145
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)39.670, 47.873, 77.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Myoglobin


Mass: 17414.064 Da / Num. of mol.: 1 / Mutation: L29H, F33Y, F43H, I107E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter macrocephalus (sperm whale) / Gene: MB / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.07 % / 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, to yield ...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, to yield a final volume of 150-200uL; this was equilibrated against 30mL of same crystalization solution.

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: LN2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 4, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 25784 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.047 / Χ2: 1.666 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.47-1.513.70.53412680.804199.9
1.51-1.533.80.46212750.7921100
1.53-1.563.70.40112580.8091100
1.56-1.593.80.32612660.8491100
1.59-1.633.80.29812580.8991100
1.63-1.673.80.2412950.9481100
1.67-1.713.80.21612371.15199.9
1.71-1.753.80.1812861.1091100
1.75-1.813.80.15212771.1471100
1.81-1.863.80.12612711.3121100
1.86-1.933.80.10812861.4841100
1.93-2.013.80.0912891.6851100
2.01-2.13.80.08112862.222199.9
2.1-2.213.80.06912902.3711100
2.21-2.353.80.06312852.4831100
2.35-2.533.70.06113022.8721100
2.53-2.793.80.04813012.63199.9
2.79-3.193.70.04113152.773199.9
3.19-4.023.60.03113452.724199.8
4.02-503.40.03313942.201197.5

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Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070refinement
HKL-20002.3.1data scaling
PDB_EXTRACT3.27data extraction
HKL-20002.3.1data reduction
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FWX

4fwx


Resolution: 1.47→20.49 Å / SU ML: 0.2046 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.8457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 2289 4.74 %
Rwork0.2011 45993 -
obs0.2026 48282 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.79 Å2
Refinement stepCycle: LAST / Resolution: 1.47→20.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 43 145 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511389
X-RAY DIFFRACTIONf_angle_d1.92131887
X-RAY DIFFRACTIONf_chiral_restr0.1038192
X-RAY DIFFRACTIONf_plane_restr0.0105236
X-RAY DIFFRACTIONf_dihedral_angle_d22.4621195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50.39731270.31822519X-RAY DIFFRACTION86.53
1.5-1.540.33091400.292901X-RAY DIFFRACTION99.97
1.54-1.570.2521470.26962895X-RAY DIFFRACTION100
1.57-1.620.26171450.26352921X-RAY DIFFRACTION100
1.62-1.660.26061450.24372927X-RAY DIFFRACTION99.93
1.66-1.720.28921430.2422906X-RAY DIFFRACTION100
1.72-1.780.26421510.24672915X-RAY DIFFRACTION100
1.78-1.850.32951460.24582895X-RAY DIFFRACTION100
1.85-1.930.28691290.24162912X-RAY DIFFRACTION99.93
1.93-2.040.26731650.2192875X-RAY DIFFRACTION99.84
2.04-2.160.25991350.2072913X-RAY DIFFRACTION99.61
2.16-2.330.2331450.20482896X-RAY DIFFRACTION99.31
2.33-2.570.22341460.20022866X-RAY DIFFRACTION99.34
2.57-2.940.20391340.20362906X-RAY DIFFRACTION99.44
2.94-3.690.22461410.18362891X-RAY DIFFRACTION99.05
3.7-20.490.1931500.15672855X-RAY DIFFRACTION98.52
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)
13.00137360969-0.394606173872-0.3504490003531.65568729687-0.8449620357011.8986880046-0.1273851381740.282520387016-0.0874427694985-0.06110201771410.0695563283060.1282207878440.0146555377375-0.07779103060570.05862544034180.164323604024-0.0308433567258-0.008668618936930.132153833778-0.01544095331210.155762776271-0.8003192791522.89934556779-5.09948338334
26.0321364681-1.555273757391.203043766041.55219190238-0.7949834304662.319686630390.001181956077780.212083657456-0.621645454691-0.008594541855080.035865954870.233053393470.371327545021-0.0976301890364-0.04919031283020.211646231094-0.01192858153860.03726758685830.144450392872-0.02082530634440.242386229329-8.71464269051-4.490154488860.208935962435
33.01148628960.187547933661-0.08642359428381.78307515214-0.3254528042522.93566496513-0.1395661633960.0829105208174-0.1362648423290.09525812939710.0325417207157-0.0910487145841-0.07435219044090.08839730555770.1012451594520.1723571282360.0153951507767-0.02490454742740.1603104182690.007717943208020.2055231197635.224953071830.409120807117-0.199020373401
42.465793423713.74750171421-0.7685562674185.70712453255-1.183718833060.259000980833-0.3514858745530.09408689996940.109055952870.205642025635-0.1242881036990.4501334379350.445025137682-0.2880991904430.3664034037940.4497058338930.01362252399510.02049091045430.747592914824-0.1634385193270.364130106162-4.777022770757.64148793992-18.1245924752
53.64839581105-1.42635212289-0.7157695085376.5082640992-0.671951026941.699434606940.3179226186680.764369158299-0.0653697798602-0.875250213724-0.3396337739010.1039139894580.268831548289-0.365854434965-0.02007008043630.3232358908620.002991069238230.01381768412690.706195992541-0.2134514789360.317786435989-3.06841303592-2.39977500536-18.6034288454
62.56553836944-1.49930790222-2.119539042682.941873806841.08072422122.90299006260.1867433444030.266082439707-0.054191515887-0.690061519942-0.4710732938190.550667442882-0.0176097137462-1.377986531950.1715691543350.3665814329270.179275480843-0.0891331018040.617048351811-0.04675986160130.2829347538483.348977462896.69377976822-22.790069027
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 52 through 124 )52 - 12452 - 124
22chain 'A' and (resid 125 through 153 )125 - 153125 - 153
33chain 'A' and (resid 1 through 35 )1 - 351 - 35
44chain 'A' and (resid 42 through 45 )42 - 4542 - 45
55chain 'A' and (resid 36 through 41 )36 - 4136 - 41
66chain 'A' and (resid 46 through 51 )46 - 5146 - 51

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