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- PDB-5vzq: Sperm whale myoglobin V68A/I107Y with nitric oxide -

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Basic information

Entry
Database: PDB / ID: 5vzq
TitleSperm whale myoglobin V68A/I107Y with nitric oxide
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / nitrosyl / nitric oxide
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
Model detailsThis stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale ...This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale myoglobin ferric H64A and N-hydroxyamphetamine.
AuthorsWang, B. / Thomas, L.M. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1213674 United States
CitationJournal: Biochemistry / Year: 2018
Title: Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets.
Authors: Wang, B. / Shi, Y. / Tejero, J. / Powell, S.M. / Thomas, L.M. / Gladwin, M.T. / Shiva, S. / Zhang, Y. / Richter-Addo, G.B.
History
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)18,1765
Polymers17,3871
Non-polymers7894
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-31 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.816, 29.321, 63.923
Angle α, β, γ (deg.)90.000, 105.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin /


Mass: 17387.127 Da / Num. of mol.: 1 / Mutation: V68A/I107Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185

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Non-polymers , 5 types, 100 molecules

#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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.82 Å3/Da / Density % sol: 32.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, 1 mM EDTA, pH 7.4 2.56 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 11655 / % possible obs: 97 % / Redundancy: 3 % / Rmerge(I) obs: 0.027 / Rpim(I) all: 0.018 / Rrim(I) all: 0.033 / Χ2: 2.75 / Net I/av σ(I): 49.271 / Net I/σ(I): 49.1 / Num. measured all: 35049
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.8220.0420.9950.0330.0542.66591.9
1.82-1.852.30.0430.9960.0330.0552.69596.3
1.85-1.892.50.0430.9950.030.0532.90596.7
1.89-1.932.90.0420.9960.0290.0513.10998
1.93-1.9730.040.9970.0270.0483.04297.8
1.97-2.0230.0350.9980.0240.0432.56598
2.02-2.0730.0330.9980.0210.0392.67497
2.07-2.123.20.0330.9980.0210.0392.88298.1
2.12-2.183.20.0310.9980.020.0372.64697.5
2.18-2.263.30.0310.9990.020.0382.83896.9
2.26-2.343.30.0310.9980.020.0372.88596.8
2.34-2.433.40.0280.9990.0180.0342.73697.5
2.43-2.543.30.030.9980.0190.0362.76196.9
2.54-2.673.30.0310.9980.020.0372.73598
2.67-2.843.30.030.9980.0190.0352.6196.3
2.84-3.063.20.0270.9990.0180.0332.84997.5
3.06-3.373.20.0250.9990.0160.032.47996.4
3.37-3.863.10.0250.9990.0160.032.45597.9
3.86-4.8630.0240.9980.0160.0292.38898.2
4.86-502.60.0220.9990.0160.0273.24196.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MBW
Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.451 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.132
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 556 4.8 %RANDOM
Rwork0.1566 ---
obs0.1589 11086 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.39 Å2 / Biso mean: 14.844 Å2 / Biso min: 6.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-0.12 Å2
2--0.71 Å20 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 53 96 1367
Biso mean--12.49 19.95 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191304
X-RAY DIFFRACTIONr_bond_other_d0.0030.021265
X-RAY DIFFRACTIONr_angle_refined_deg1.9992.0011764
X-RAY DIFFRACTIONr_angle_other_deg1.0832914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.225152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46424.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27615234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.489154
X-RAY DIFFRACTIONr_chiral_restr0.1390.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021440
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02304
X-RAY DIFFRACTIONr_mcbond_it1.6011.236612
X-RAY DIFFRACTIONr_mcbond_other1.4461.232610
X-RAY DIFFRACTIONr_mcangle_it2.2411.84762
LS refinement shellResolution: 1.789→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 40 -
Rwork0.163 801 -
all-841 -
obs--91.91 %

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