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- PDB-4f69: Carbonmonoxy structure of Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp Cer... -

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Basic information

Entry
Database: PDB / ID: 4f69
TitleCarbonmonoxy structure of Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp Cerebratulus lacteus mini-hemoglobin
ComponentsNeural hemoglobin
KeywordsOXYGEN TRANSPORT / oxygen-storage / apolar tunnel
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Neural hemoglobin
Similarity search - Component
Biological speciesCerebratulus lacteus (milky ribbon-worm)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSoman, J. / Salter, M.D. / Olson, J.S.
CitationJournal: To be Published
Title: Carbonmonoxy structure of Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp Cerebratulus lacteus mini-hemoglobin
Authors: Soman, J. / Salter, M.D. / Olson, J.S.
History
DepositionMay 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neural hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3664
Polymers11,6291
Non-polymers7373
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.650, 43.360, 59.500
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 Neural hemoglobin / NrHb


Mass: 11629.138 Da / Num. of mol.: 1 / Mutation: Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cerebratulus lacteus (milky ribbon-worm)
Production host: Escherichia coli (E. coli) / References: UniProt: O76242
#2: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: Protein crystallized from 2.5 mM Ammonium Sulfate and 0.1M sodium Citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5412 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 1.6→27.08 Å / Num. obs: 14641 / % possible obs: 97 % / Redundancy: 2.62 % / Rmerge(I) obs: 0.048 / Χ2: 0.99 / Net I/σ(I): 11.7 / Scaling rejects: 290
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.6-1.662.140.3122.6282213190.7889.7
1.66-1.722.680.2663.2376314040.7895.9
1.72-1.82.680.2273.8389614530.8596.4
1.8-1.92.690.1784.9386314350.8397.3
1.9-2.022.690.1386.6394314660.998.1
2.02-2.172.660.0979.6394714780.9698.2
2.17-2.392.670.08412398514860.9499.2
2.39-2.742.660.06315.4403815040.9199
2.74-3.452.660.05820.8412015261.199.7
3.45-27.082.580.04233.5421015701.796.4

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.8.9 W9RSSIdata reduction
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→27.076 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.845 / SU ML: 0.63 / σ(F): 1.42 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 1464 10 %
Rwork0.2065 --
obs0.2091 14636 96.97 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.372 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 64.47 Å2 / Biso mean: 23.9547 Å2 / Biso min: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1-9.096 Å2-0 Å2-0 Å2
2---2.8725 Å2-0 Å2
3----6.2235 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 51 125 997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008899
X-RAY DIFFRACTIONf_angle_d0.9731227
X-RAY DIFFRACTIONf_chiral_restr0.06119
X-RAY DIFFRACTIONf_plane_restr0.004155
X-RAY DIFFRACTIONf_dihedral_angle_d14.584295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6003-1.65750.47771320.48171187131990
1.6575-1.72380.42731400.37461265140596
1.7238-1.80220.36611450.30931306145196
1.8022-1.89720.30991440.2341291143597
1.8972-2.01610.23421470.20131318146598
2.0161-2.17170.22351470.18981331147898
2.1717-2.39010.25071490.18621337148699
2.3901-2.73570.19921500.20041354150499
2.7357-3.44550.22051530.178813721525100
3.4455-27.07940.21570.19841411156896

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