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- PDB-4f6d: Oxy structure of His100Phe Cerebratulus lacteus mini-hemoglobin -

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Basic information

Entry
Database: PDB / ID: 4f6d
TitleOxy structure of His100Phe 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 / 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 His100Phe 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)12,2043
Polymers11,5561
Non-polymers6482
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.528, 43.485, 59.498
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: 11555.977 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-OXY / OXYGEN MOLECULE


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


Mass: 18.015 Da / Num. of mol.: 164 / 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: 48.33 %
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 / 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→100 Å / Num. obs: 10039 / % possible obs: 93.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.046 / Χ2: 3.639 / Net I/σ(I): 41.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.832.60.0984973194.1
1.83-1.862.50.094833.051194.7
1.86-1.92.50.0844853.452191.9
1.9-1.942.50.0785063.23194.2
1.94-1.982.60.0744803.423191.8
1.98-2.032.50.0644973.491194
2.03-2.082.50.0614793.551192.6
2.08-2.132.50.0595003.823195.8
2.13-2.22.50.0564823.781191.5
2.2-2.272.50.0535043.745195.1
2.27-2.352.50.0564983.85193.6
2.35-2.442.50.0514933.958192.1
2.44-2.552.50.0515073.919195.3
2.55-2.692.50.054963.967193.4
2.69-2.862.50.0485153.877196.1
2.86-3.082.50.0455104.069193.4
3.08-3.392.50.0425083.73193.9
3.39-3.882.40.045263.862194.3
3.88-4.892.50.0395253.527193.8
4.89-1002.40.0375483.449189.3

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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: 1.8→27.074 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8803 / SU ML: 0.12 / σ(F): 1.36 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1971 1004 10.02 %
Rwork0.1688 --
obs0.1716 10018 93.69 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.641 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 42.84 Å2 / Biso mean: 16.1123 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.1705 Å20 Å20 Å2
2---0.2952 Å20 Å2
3---0.1247 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 45 164 1024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025894
X-RAY DIFFRACTIONf_angle_d0.9221223
X-RAY DIFFRACTIONf_chiral_restr0.059119
X-RAY DIFFRACTIONf_plane_restr0.003157
X-RAY DIFFRACTIONf_dihedral_angle_d14.651298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8004-1.89530.24741400.17291261140193
1.8953-2.0140.22291380.16321244138293
2.014-2.16940.19471430.17271277142094
2.1694-2.38760.21691410.16331274141594
2.3876-2.73280.2081440.16611286143094
2.7328-3.4420.18981450.16871307145295
3.442-27.07730.17011530.17191365151893

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