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- PDB-4f6g: Aquomet Structure of His100Trp Cerebratulus lacteus mini-hemoglobin -

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Basic information

Entry
Database: PDB / ID: 4f6g
TitleAquomet Structure of His100Trp 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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Neural hemoglobin
Similarity search - Component
Biological speciesCerebratulus lacteus (milky ribbon-worm)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.64 Å
AuthorsSoman, J. / Salter, M.D. / Olson, J.S.
CitationJournal: To be Published
Title: Aquomet Structure of His100Trp 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 1.1Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: Neural hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4004
Polymers11,5951
Non-polymers8053
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.680, 43.470, 59.480
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: 11595.012 Da / Num. of mol.: 1 / Mutation: His100Phe
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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 48.3 %
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: OTHER / 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: 1.64→50 Å / Num. obs: 13828 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Χ2: 1.343 / Net I/σ(I): 49.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.64-1.673.40.1126761.992198.1
1.67-1.73.50.1016791.919198.3
1.7-1.733.50.0876721.807198.4
1.73-1.773.50.0866551.734197.9
1.77-1.813.50.0836941.833197.5
1.81-1.853.40.0766801.652197.3
1.85-1.893.40.0716691.637197
1.89-1.943.30.0646671.619197.4
1.94-23.30.066671.405198.2
2-2.073.30.0567001.41197.8
2.07-2.143.20.0536831.225198.6
2.14-2.233.20.0516801.223198.1
2.23-2.333.20.0486911.129197.6
2.33-2.453.20.0517081.14199.4
2.45-2.63.20.0516851.064198.7
2.6-2.83.30.0496960.957198.4
2.8-3.093.30.0497160.9198.5
3.09-3.533.30.0467130.774198.3
3.53-4.453.40.0457180.706198.6
4.45-503.30.0487790.737196.5

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
d*TREKdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.64→24.545 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8779 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 18.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 1379 10 %
Rwork0.1841 --
obs0.1863 13789 97.95 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.598 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 49.9 Å2 / Biso mean: 18.6524 Å2 / Biso min: 5.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.6859 Å2-0 Å20 Å2
2---3.0175 Å20 Å2
3---3.7034 Å2
Refinement stepCycle: LAST / Resolution: 1.64→24.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 54 141 1013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007911
X-RAY DIFFRACTIONf_angle_d0.9661246
X-RAY DIFFRACTIONf_chiral_restr0.068119
X-RAY DIFFRACTIONf_plane_restr0.004158
X-RAY DIFFRACTIONf_dihedral_angle_d14.155300
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 (%)
1.6404-1.6990.31271350.30251208134397
1.699-1.7670.30091330.24431195132898
1.767-1.84740.25111370.21631232136997
1.8474-1.94470.20991340.17951203133797
1.9447-2.06650.20531360.17091226136298
2.0665-2.2260.18291370.16911232136998
2.226-2.44980.18021400.17461254139499
2.4498-2.80390.19941380.18151241137999
2.8039-3.53090.20561430.18231278142198
3.5309-24.54810.19481460.17311341148798
Refinement TLS params.Method: refined / Origin x: 30.8678 Å / Origin y: 36.1966 Å / Origin z: 10.7037 Å
111213212223313233
T0.0673 Å2-0.0052 Å20.0004 Å2-0.087 Å20.0006 Å2--0.0838 Å2
L0.3681 °20.1692 °2-0.481 °2-0.5842 °2-0.1017 °2--0.7427 °2
S-0.0003 Å °-0.0458 Å °0.0157 Å °0.0348 Å °0.0122 Å °-0.0119 Å °0.0135 Å °0.1265 Å °-0.0172 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 201
2X-RAY DIFFRACTION1allA202 - 1112
3X-RAY DIFFRACTION1allA1 - 441

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