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- PDB-4f68: Oxy structure of Tyr11Phe/Gln44Leu/Thr48Val/Ala55Trp Cerebratulus... -

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Basic information

Entry
Database: PDB / ID: 4f68
TitleOxy 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-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Neural hemoglobin
Similarity search - Component
Biological speciesCerebratulus lacteus (milky ribbon-worm)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsSoman, J. / Salter, M.D. / Olson, J.S.
CitationJournal: To be Published
Title: Oxy 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Neural hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2783
Polymers11,6291
Non-polymers6482
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.620, 43.550, 59.750
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: 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-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-OXY / OXYGEN MOLECULE / Oxygen


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: Protein crystallized from 2.2mM Ammonium Sulfate and 0.2M Sodium thiocyanate, 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 / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 1.8→24.46 Å / Num. obs: 10650 / % possible obs: 98.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.039 / Χ2: 1.01 / Net I/σ(I): 14.3 / Scaling rejects: 194
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.8-1.862.340.2254.1248310581.02100
1.86-1.942.370.2444.8250010500.9699.8
1.94-2.032.370.1595.8252710611.03100
2.03-2.132.370.1267.2251910540.9699.8
2.13-2.272.390.11410.2254210541.0299.8
2.27-2.442.40.07512.9258710711.0299.8
2.44-2.692.40.05916.2257210591.0199.4
2.69-3.082.410.04920264910880.9999.5
3.08-3.872.440.03527.3265610820.9598.3
3.87-24.462.460.03332.9267610731.1392.6

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9.8.9 W9RSSIdata reduction
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→24.46 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.856 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1063 9.99 %
Rwork0.2013 --
obs0.2034 10643 98.77 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.875 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 67.38 Å2 / Biso mean: 24.4324 Å2 / Biso min: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1-5.3757 Å20 Å20 Å2
2---2.2187 Å2-0 Å2
3----3.1569 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 45 116 982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007894
X-RAY DIFFRACTIONf_angle_d0.9561222
X-RAY DIFFRACTIONf_chiral_restr0.06119
X-RAY DIFFRACTIONf_plane_restr0.004155
X-RAY DIFFRACTIONf_dihedral_angle_d14.851293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.8820.32271300.286911781308100
1.882-1.98120.32041320.235811891321100
1.9812-2.10520.26491310.20711801311100
2.1052-2.26770.19451330.198411971330100
2.2677-2.49570.2371330.194412021335100
2.4957-2.85640.25521350.20831208134399
2.8564-3.59690.20711330.19571210134399
3.5969-24.46570.1841360.18891216135294

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