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- PDB-1f6h: COMBINED RIETVELD AND STEREOCHEMICAL RESTRAINT REFINEMENT OF A PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1f6h
TitleCOMBINED RIETVELD AND STEREOCHEMICAL RESTRAINT REFINEMENT OF A PROTEIN
ComponentsMYOGLOBIN (MET)
KeywordsOXYGEN STORAGE/TRANSPORT / POWDER DIFFRACTION / RIETVELD REFINEMENT / MYOBLOBIN(MET) / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodPOWDER DIFFRACTION / SYNCHROTRON / Resolution: 3.31 Å
AuthorsVon Dreele, R.B.
CitationJournal: J.APPL.CRYSTALLOGR. / Year: 1999
Title: Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure
Authors: Von Dreele, R.B.
History
DepositionJun 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 (MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8512
Polymers17,2351
Non-polymers6161
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein MYOGLOBIN (MET)


Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.15 % / Description: SECOND PHASE OF (NH4)2SO4 IN SAMPLE
Crystal growTemperature: 300 K / Method: grinding / pH: 6.37
Details: saturated ammonium sulphate, sodium dihydrogen phosphate, dipotassium phosphate, powder slurry in 1.5mm capillary, 4mm long, pH 6.37, grinding, temperature 300K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
24 M11Na2HPO4/K2HPO4
1ammonium sulfate11

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3B1 / Wavelength: 1.14991
DetectorDetector: SCINTILLATOR / Date: Mar 20, 1998 / Details: 2MM X 8MM BEAM ANALYZER : GE(111)
RadiationMonochromator: DOUBLE SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthWavelength: 1.14991 Å / Relative weight: 1
ReflectionResolution: 3.31→47.06 Å / Num. all: 2088 / Num. obs: 2088 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1 %

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Processing

Software
NameClassification
GSASrefinement
PROCESSdata scaling
RefinementResolution: 3.31→47.06 Å / σ(F): 0
Stereochemistry target values: Engh & Huber bonds and angles, peptide planes, aromatic planes, minimum van der Waals contacts, H-bond contacts, torsion angle pseudopotentials
Details: powder pattern Rwp=0.0230, Rp=0.0168, Nobs=4648 powder profile points
RfactorNum. reflection% reflectionSelection details
all0.035 2088 --
obs0.035 2088 100 %-
Rfree---R-factor on F**2 extracted from powder data during Rietveld refinement
Refinement stepCycle: LAST / Resolution: 3.31→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 44 0 1261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.023
X-RAY DIFFRACTIONo_angle_deg1.63
X-RAY DIFFRACTIONo-antibump (A)0.049
X-RAY DIFFRACTIONo-Hbond (A)0.199
X-RAY DIFFRACTIONo-chiral volume A**30.153
X-RAY DIFFRACTIONo-torsion_deg4.33
X-RAY DIFFRACTIONo-torsion_pseudopotentials1.41
Software
*PLUS
Name: GSAS / Classification: refinement
Refine LS restraints
*PLUS
Type: x_chiral_restr / Dev ideal: 0.153

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