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- PDB-1m3w: Crystal Structure of a Molecular Maquette Scaffold -

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Basic information

Entry
Database: PDB / ID: 1m3w
TitleCrystal Structure of a Molecular Maquette Scaffold
ComponentsH10H24
KeywordsDE NOVO PROTEIN / four-helix bundle / heme binding / maquette / heme binding protein / electron transport
Function / homology:
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsHuang, S.S. / Gibney, B.R. / Stayrook, S.E. / Dutton, P.L. / Lewis, M.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: X-ray Structure of a Maquette Scaffold
Authors: Huang, S.S. / Gibney, B.R. / Stayrook, S.E. / Dutton, P.L. / Lewis, M.
History
DepositionJul 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H10H24
B: H10H24
C: H10H24
D: H10H24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6276
Polymers15,2264
Non-polymers4012
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-119 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.900, 48.800, 46.700
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
H10H24


Mass: 3806.542 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED BY Solid phase protein synthesis using Fmoc protected amino acids.
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg

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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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000MME, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Temperature: 28 ℃ / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %(w/v)PEG2000 MME1reservoir
20.1 MHEPES1reservoirpH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.98245, 1.00191, 1.009757
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 12, 2000
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.982451
21.001911
31.0097571
ReflectionResolution: 2.73→20 Å / Num. all: 4649 / Num. obs: 3188 / % possible obs: 86.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 90.3 Å2 / Rsym value: 0.047 / Net I/σ(I): 23.3
Reflection shellResolution: 2.73→2.83 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 12 / Num. unique all: 324 / Rsym value: 0.105 / % possible all: 96.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→9.99 Å / Rfactor Rfree error: 0.024 / Data cutoff high absF: 618561.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: bulk solvent correction by CNS1.1, density level 0.44 e/A^3, B-factor 36.7456 A^2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 135 4.8 %RANDOM
Rwork0.234 ---
all0.2357 2822 --
obs0.234 2820 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.8175 Å2 / ksol: 0.447641 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.86 Å20 Å28.61 Å2
2---5.83 Å20 Å2
3----3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.8→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 2 0 1046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.781.5
X-RAY DIFFRACTIONc_mcangle_it5.852
X-RAY DIFFRACTIONc_scbond_it4.692
X-RAY DIFFRACTIONc_scangle_it5.152.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.082 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 17 3.8 %
Rwork0.285 430 -
obs--93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CAPPING.PARAMCAPPING.TOP

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