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- PDB-4f6i: Oxy Structure of His100Trp Cerebratulus lacteus mini-hemoglobin -

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Basic information

Entry
Database: PDB / ID: 4f6i
TitleOxy 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 / Globin / Globin-like / 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: 1.56 Å
AuthorsSoman, J. / Salter, M.D. / Olson, J.S.
CitationJournal: To be Published
Title: Oxy 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

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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)12,2433
Polymers11,5951
Non-polymers6482
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)42.150, 43.390, 59.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Neural hemoglobin / NrHb


Mass: 11595.012 Da / Num. of mol.: 1 / Mutation: His100Trp
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.: 143 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 298 K / pH: 5.4
Details: Protein crystallized from 2.5 mM Ammonium Sulfate and 0.1M sodium Citrate, pH 5.4, 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: 1.56→26.98 Å / Num. obs: 15356 / % possible obs: 95 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.044 / Χ2: 1.01 / Net I/σ(I): 11.1 / Scaling rejects: 280
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.56-1.621.790.4452.1194510881.0168.6
1.62-1.682.270.3243.2338114810.9893.7
1.68-1.762.440.2574.138451570197.8
1.76-1.852.440.1965.2382215591.0598.5
1.85-1.972.440.1436.7384315650.9798.6
1.97-2.122.480.1068.8396615960.9599.4
2.12-2.332.470.08711.2400116070.9599.4
2.33-2.672.490.06714.5404016030.9799.4
2.67-3.362.490.05319.7412616391.0499.3
3.36-26.982.50.04228.4418716481.1895

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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: 1.56→26.974 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8573 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 1535 10 %
Rwork0.1978 --
obs0.1996 15350 94.96 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.133 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 60.33 Å2 / Biso mean: 26.3021 Å2 / Biso min: 13.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.9969 Å2-0 Å2-0 Å2
2---1.2031 Å20 Å2
3---0.2062 Å2
Refinement stepCycle: LAST / Resolution: 1.56→26.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 45 143 1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01890
X-RAY DIFFRACTIONf_angle_d0.9021216
X-RAY DIFFRACTIONf_chiral_restr0.057118
X-RAY DIFFRACTIONf_plane_restr0.003155
X-RAY DIFFRACTIONf_dihedral_angle_d14.224293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5599-1.61030.6496980.619388197967
1.6103-1.66780.51541330.46391195132892
1.6678-1.73460.39161400.38071258139897
1.7346-1.81350.3181420.31271273141598
1.8135-1.90910.24871400.25161279141998
1.9091-2.02870.26781460.19591309145599
2.0287-2.18520.17851450.17431303144899
2.1852-2.4050.20751440.18031307145199
2.405-2.75280.18121480.183713291477100
2.7528-3.4670.20571490.17791337148699
3.467-26.97780.17941500.17151344149494
Refinement TLS params.Method: refined / Origin x: 30.6777 Å / Origin y: 35.6002 Å / Origin z: 10.7518 Å
111213212223313233
T0.1564 Å20.0006 Å20.0101 Å2-0.1666 Å2-0.0018 Å2--0.1754 Å2
L0.6895 °20.3688 °2-0.502 °2-0.3875 °2-0.0208 °2--0.7527 °2
S-0.0145 Å °-0.0677 Å °0.012 Å °-0.0146 Å °0.0291 Å °-0.0023 Å °0.0649 Å °0.1111 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 201
2X-RAY DIFFRACTION1all150
3X-RAY DIFFRACTION1allA1 - 443

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