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- PDB-1ux9: Mapping protein matrix cavities in human cytoglobin through Xe at... -

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Basic information

Entry
Database: PDB / ID: 1ux9
TitleMapping protein matrix cavities in human cytoglobin through Xe atom binding: a crystallographic investigation
ComponentsCYTOGLOBIN
KeywordsOXYGEN TRANSPORT / OXYGEN STORAGE/TRANSPORT / HEME / TRANSPORT
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor / fatty acid peroxidase activity / negative regulation of hepatic stellate cell activation / oxidoreductase activity, acting on a heme group of donors / Intracellular oxygen transport / nitric oxide catabolic process / negative regulation of collagen biosynthetic process / carbon monoxide binding / negative regulation of fibroblast migration / catalase activity ...Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor / fatty acid peroxidase activity / negative regulation of hepatic stellate cell activation / oxidoreductase activity, acting on a heme group of donors / Intracellular oxygen transport / nitric oxide catabolic process / negative regulation of collagen biosynthetic process / carbon monoxide binding / negative regulation of fibroblast migration / catalase activity / superoxide dismutase / superoxide dismutase activity / fatty acid oxidation / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / eNOS activation / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / response to oxidative stress / response to hypoxia / oxidoreductase activity / neuron projection / iron ion binding / neuronal cell body / heme binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Globin, lamprey/hagfish type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXACYANOFERRATE(3-) / PROTOPORPHYRIN IX CONTAINING FE / XENON / Cytoglobin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDe Sanctis, D. / Dewilde, S. / Pesce, A. / Moens, L. / Ascenzi, P. / Hankeln, T. / Burmester, T. / Bolognesi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Mapping Protein Matrix Cavities in Human Cytoglobin Through Xe Atom Binding
Authors: De Sanctis, D. / Dewilde, S. / Pesce, A. / Moens, L. / Ascenzi, P. / Hankeln, T. / Burmester, T. / Bolognesi, M.
History
DepositionFeb 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOGLOBIN
B: CYTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,37913
Polymers42,8032
Non-polymers2,57611
Water66737
1
A: CYTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7557
Polymers21,4011
Non-polymers1,3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6246
Polymers21,4011
Non-polymers1,2225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.840, 70.520, 98.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98863, 0.12126, -0.08888), (0.13156, 0.41157, -0.90183), (-0.07277, -0.90328, -0.42284)
Vector: 41.31231, 29.52729, 51.51895)

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Components

#1: Protein CYTOGLOBIN / / HISTOGLOBIN / HGB / STELLATE CELL ACTIVATION-ASSOCIATED-PROTEIN / CYGB / STAP


Mass: 21401.484 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8WWM9
#2: Chemical
ChemComp-XE / XENON / Xenon


Mass: 131.293 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Xe
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6FeN6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, CYS 38 TO SER 38 ENGINEERED MUTATION IN CHAIN A, CYS 83 TO SER 83 ...ENGINEERED MUTATION IN CHAIN A, CYS 38 TO SER 38 ENGINEERED MUTATION IN CHAIN A, CYS 83 TO SER 83 ENGINEERED MUTATION IN CHAIN B, CYS 38 TO SER 38 ENGINEERED MUTATION IN CHAIN B, CYS 83 TO SER 83

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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: 35 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorDate: Aug 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 22810 / % possible obs: 98.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.8 Å / SU B: 8.078 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.519 / ESU R Free: 0.266 / Details: TLS
RfactorNum. reflection% reflectionSelection details
Rfree0.23804 664 5 %RANDOM
Rwork0.19163 ---
obs0.19391 12724 98.35 %-
Displacement parametersBiso mean: 26.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 119 37 2620

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