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- PDB-1kr7: Crystal structure of the nerve tissue mini-hemoglobin from the ne... -

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Basic information

Entry
Database: PDB / ID: 1kr7
TitleCrystal structure of the nerve tissue mini-hemoglobin from the nemertean worm Cerebratulus lacteus
ComponentsNeural globin
KeywordsOXYGEN STORAGE/TRANSPORT / nerve tissue / mini-hemoglobin / protein cavities / Oxygen transport / OXYGEN STORAGE-TRANSPORT COMPLEX
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Neural hemoglobin
Similarity search - Component
Biological speciesCerebratulus lacteus (milky ribbon-worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsPesce, A. / Nardini, M. / Dewilde, S. / Geuens, E. / Yamauchi, k. / Ascenzi, P. / Riggs, A.F. / Moens, L. / Bolognesi, M.
Citation
Journal: Structure / Year: 2002
Title: The 109 residue nerve tissue minihemoglobin from Cerebratulus lacteus highlights striking structural plasticity of the alpha-helical globin fold
Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Geuens, E. / Yamauchi, k. / Ascenzi, P. / Riggs, A.F. / Moens, L. / Bolognesi, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray analysis of neural hemoglobin from the nemertean worm Cerebratulus lacteus
Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Ascenzi, P. / Riggs, A.F. / Yamauchi, K. / Geuens, E. / Moens, L. / Bolognesi, M.
History
DepositionJan 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3515
Polymers11,5471
Non-polymers8044
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.721, 43.173, 60.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neural globin / Mini-hemoglobin


Mass: 11546.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cerebratulus lacteus (milky ribbon-worm)
Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: O76242

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Non-polymers , 5 types, 110 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
127 mg/mlprotein1drop
260 %ammonium sulfate1reservoir
350 mMsodium acetate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.739, 1.740, 0.915
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2001 / Details: mirrors
RadiationMonochromator: Si 311 channel and Si 111 channel cut / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7391
21.741
30.9151
ReflectionResolution: 1.5→35 Å / Num. all: 17906 / Num. obs: 17906 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 14.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1168 / Rsym value: 0.239 / % possible all: 95.7
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 35 Å / Num. measured all: 67606 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.239

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→35.14 Å / SU B: 2.82431 / SU ML: 0.04376 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08727 / ESU R Free: 0.07211 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.18702 1808 -RANDOM
Rwork0.15298 ---
all0.1563 17906 --
obs0.1563 16071 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 16.023 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 54 106 974
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.021
X-RAY DIFFRACTIONp_mcbond_it1.1881
X-RAY DIFFRACTIONp_mcangle_it2.0932
X-RAY DIFFRACTIONp_scbond_it3.2463
X-RAY DIFFRACTIONp_scangle_it4.3333
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 35 Å / Rfactor all: 0.1563 / Rfactor obs: 0.153 / Rfactor Rfree: 0.18702 / Rfactor Rwork: 0.15298
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.14

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