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- PDB-1v07: CRYSTAL STRUCTURE OF ThrE11Val mutant of THE NERVE TISSUE MINI-HE... -

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Entry
Database: PDB / ID: 1v07
TitleCRYSTAL STRUCTURE OF ThrE11Val mutant of THE NERVE TISSUE MINI-HEMOGLOBIN FROM THE NEMERTEAN WORM CEREBRATULUS LACTEUS
ComponentsNEURAL HEMOGLOBIN
KeywordsOXYGEN TRANSPORT / OXYGEN AFFINITY OF C.LACTEUS MINI-HEMOGLOBIN / NERVE TISSUE MINI-HEMOGLOBIN
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 / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsPesce, A. / Nardini, M. / Ascenzi, P. / Geuens, E. / Dewilde, S. / Moens, L. / Bolognesi, M. / Riggs, A. / Hale, A. / Deng, P. ...Pesce, A. / Nardini, M. / Ascenzi, P. / Geuens, E. / Dewilde, S. / Moens, L. / Bolognesi, M. / Riggs, A. / Hale, A. / Deng, P. / Nienhaus, G.U. / Olson, J.S. / Nienhaus, K.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Thr-E11 Regulates O2 Affinity in Cerebratulus Lacteus Mini-Hemoglobin
Authors: Pesce, A. / Nardini, M. / Ascenzi, P. / Geuens, E. / Dewilde, S. / Moens, L. / Bolognesi, M. / Riggs, A. / Hale, A. / Deng, P. / Nienhaus, G.U. / Olson, J.S. / Nienhaus, K.
History
DepositionMar 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)12,2904
Polymers11,5451
Non-polymers7453
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.656, 43.422, 59.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NEURAL HEMOGLOBIN / NRHB


Mass: 11544.977 Da / Num. of mol.: 1 / Mutation: YES
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
#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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, THR 48 TO VAL 48 FUNCTION: ACTS AS AN OXYGEN STORE CAPABLE OF ...ENGINEERED MUTATION IN CHAIN A, THR 48 TO VAL 48 FUNCTION: ACTS AS AN OXYGEN STORE CAPABLE OF SUSTAINING NEURONAL ACTIVITY IN AN ANOXIC ENVIRONMENT FOR 5 TO 30 MIN.

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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 growpH: 6 / Details: AMMONIUM SULFATE, SODIUM ACETATE, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 11, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 12524 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 5 / % possible all: 95.4

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.7→30 Å / SU B: 1.735 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.19526 1263 10 %RANDOM
Rwork0.16737 ---
obs0.17025 11236 100 %-
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 50 92 956

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