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- PDB-1cq2: NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.... -

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Basic information

Entry
Database: PDB / ID: 1cq2
TitleNEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0 ANGSTROM
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / HELICAL / GLOBULAR / ALL-HYDROGEN CONTAINING STRUCTURE / OXYGEN STORAGE-TRANSPORT COMPLEX
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
DEUTERATED WATER / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 2 Å
AuthorsShu, F. / Ramakrishnan, V. / Schoenborn, B.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin.
Authors: Shu, F. / Ramakrishnan, V. / Schoenborn, B.P.
History
DepositionAug 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8512
Polymers17,2351
Non-polymers6161
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.530, 30.910, 34.780
Angle α, β, γ (deg.)90.00, 105.82, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein MYOGLOBIN /


Mass: 17234.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEIN IS FULLY DEUTERATED / Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid details: USING T7 EXPRESSION SYSTEM / Plasmid: PET15A / Production host: Escherichia coli (E. coli) / 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-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: SODIUM/POTASSIUM PHOSPHATE, AMMONIUM SULFATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
245 %satammonium sulfate1drop
350 mM1dropNa/K PO4
470 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR
Type: HIGH FLUX BEAM REACTOR AT BROOKHAVEN NATIONAL LABORATORY
Wavelength: 1
DetectorType: MULTI-WIRE DETECTOR FOR NEUTRONS / Detector: AREA DETECTOR / Date: Jan 5, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→62 Å / Num. all: 15372 / Num. obs: 8685 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.12 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.158 / % possible all: 92.5
Reflection shell
*PLUS
% possible obs: 92.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementResolution: 2→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED OMIT MAP TO DETERMINE PROTONATION STATES OF HISTINDINES
RfactorNum. reflection% reflectionSelection details
Rfree0.25 836 10 %RANDOM
Rwork0.16 ---
all0.16 ---
obs0.16 8360 96.3 %-
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 43 69 1329
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONx_bond_d0.015
NEUTRON DIFFRACTIONx_bond_d_na
NEUTRON DIFFRACTIONx_bond_d_prot
NEUTRON DIFFRACTIONx_angle_d
NEUTRON DIFFRACTIONx_angle_d_na
NEUTRON DIFFRACTIONx_angle_d_prot
NEUTRON DIFFRACTIONx_angle_deg1.5
NEUTRON DIFFRACTIONx_angle_deg_na
NEUTRON DIFFRACTIONx_angle_deg_prot
NEUTRON DIFFRACTIONx_dihedral_angle_d
NEUTRON DIFFRACTIONx_dihedral_angle_d_na
NEUTRON DIFFRACTIONx_dihedral_angle_d_prot
NEUTRON DIFFRACTIONx_improper_angle_d
NEUTRON DIFFRACTIONx_improper_angle_d_na
NEUTRON DIFFRACTIONx_improper_angle_d_prot
NEUTRON DIFFRACTIONx_mcbond_it
NEUTRON DIFFRACTIONx_mcangle_it
NEUTRON DIFFRACTIONx_scbond_it
NEUTRON DIFFRACTIONx_scangle_it

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