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- PDB-2bwh: Laue Structure of a Short Lived State of L29W Myoglobin -

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Basic information

Entry
Database: PDB / ID: 2bwh
TitleLaue Structure of a Short Lived State of L29W Myoglobin
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / LAUE CRYSTALLOGRAPHY / L29W MYOGLOBIN / TIME-RESOLVED X-RAY STRUCTURE DETERMINATION
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsSchmidt, M. / Nienhaus, K. / Pahl, R. / Krasselt, A. / Anderson, S. / Parak, F. / Nienhaus, G.U. / Srajer, V.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2005
Title: Ligand migration pathway and protein dynamics in myoglobin: a time-resolved crystallographic study on L29W MbCO.
Authors: Schmidt, M. / Nienhaus, K. / Pahl, R. / Krasselt, A. / Anderson, S. / Parak, F. / Nienhaus, G.U. / Srajer, V.
History
DepositionJul 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2005Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: citation / diffrn_radiation ...citation / diffrn_radiation / entity / entity_src_gen / pdbx_entity_src_syn / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _entity.pdbx_description / _entity.pdbx_mutation / _entity.src_method / _software.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9523
Polymers17,3071
Non-polymers6442
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.870, 91.870, 46.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Myoglobin /


Mass: 17307.020 Da / Num. of mol.: 1 / Mutation: L29W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02185
#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-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN M, LEU 29 TO TRP

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 57.2 %
Description: EXTRAPOLATED STRUCTURE FACTORS FROM ADDING AVERAGED DIFFERENCE STRUCTURE FACTORS TO STRUCTURE FACTORS CALCULATED FROM THE DARK STATE L29W MODEL. AVERAGED DIFFERENCE STRUCTURE FACTORS ...Description: EXTRAPOLATED STRUCTURE FACTORS FROM ADDING AVERAGED DIFFERENCE STRUCTURE FACTORS TO STRUCTURE FACTORS CALCULATED FROM THE DARK STATE L29W MODEL. AVERAGED DIFFERENCE STRUCTURE FACTORS WERE CALCULATED BY FOURIER INVERSION OF AN AVERAGE OF 6 DIFFERENCE ELECTRON DENSITY MAPS IN THE TIME-RANGE 1 MICRO- SEC TO 100 MICRO-SEC.
Crystal growpH: 7.8 / Details: pH 7.80

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 20, 2003 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 17619 / % possible obs: 100 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.94 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
Precognitiondata reduction
LaueViewdata reduction
Epinormdata scaling
LaueViewdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.9→15 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 857 4.9 %RANDOM
Rwork0.2299 ---
obs0.2299 17619 100 %-
Solvent computationSolvent model: FLAT MODEL DENSITY / Bsol: 300 Å2 / ksol: 1.56593 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.027 Å2-4.876 Å20 Å2
2--0.027 Å20 Å2
3----0.054 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å1.8 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 45 101 1369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
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_deg0.97
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→1.94 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.308 60 5.2 %
Rwork0.282 1101 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM19X.HEMETOPH19XAO.HEME

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