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- PDB-1oj6: Human brain neuroglobin three-dimensional structure -

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Basic information

Entry
Database: PDB / ID: 1oj6
TitleHuman brain neuroglobin three-dimensional structure
ComponentsNeuroglobin
KeywordsOXYGEN TRANSPORT / NEUROGLOBIN / HEME HEXACOORDINATION
Function / homology
Function and homology information


Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hypoxia / response to hypoxia / mitochondrial matrix ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hypoxia / response to hypoxia / mitochondrial matrix / heme binding / metal ion binding / cytosol
Similarity search - Function
: / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsPesce, A. / Dewilde, S. / Nardini, M. / Moens, L. / Ascenzi, P. / Hankeln, T. / Burmester, T. / Bolognesi, M.
CitationJournal: Structure / Year: 2003
Title: Human Brain Neuroglobin Structure Reveals a Distinct Mode of Controlling Oxygen Affinity
Authors: Pesce, A. / Dewilde, S. / Nardini, M. / Moens, L. / Ascenzi, P. / Hankeln, T. / Burmester, T. / Bolognesi, M.
History
DepositionJul 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,63115
Polymers67,4934
Non-polymers3,13811
Water2,882160
1
A: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4902
Polymers16,8731
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8746
Polymers16,8731
Non-polymers1,0015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7785
Polymers16,8731
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4902
Polymers16,8731
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.598, 94.927, 67.563
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Neuroglobin


Mass: 16873.150 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NGB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9NPG2
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: INVOLVED IN OXYGEN TRANSPORT IN THE BRAIN. ENGINEERED MUTATION IN CHAINS A, B, C, D, CYS ...FUNCTION: INVOLVED IN OXYGEN TRANSPORT IN THE BRAIN. ENGINEERED MUTATION IN CHAINS A, B, C, D, CYS 46 TO GLY 46 ENGINEERED MUTATION IN CHAINS A, B, C, D, CYS 55 TO SER 55 ENGINEERED MUTATION IN CHAINS A, B, C, D, CYS 120 TO SER 120

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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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growpH: 6.5
Details: 1.4 M AMMONIUM SULPHATE, 3% ISOPROPANOL, 0.05 M SODIUM CITRATE, PH 6.5
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
133 mg/mlprotein1drop
21.4 Mammonium sulfate1reservoir
33 %(v/v)isopropanol1reservoir
40.05 Msodium citrate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.738, 1.740, 0.933
DetectorDate: Mar 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7381
21.741
30.9331
ReflectionResolution: 1.95→40 Å / Num. obs: 35871 / % possible obs: 98.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5 / % possible all: 97.9
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 40 Å / Redundancy: 2.6 % / Num. measured all: 92865 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 97.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→40 Å / SU B: 4.111 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.18 / Details: SOME ATOMS IN THIS ENTRY HAVE OCCUPANCY OF 0.00
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3604 10 %RANDOM
Rwork0.178 ---
obs0.178 35871 98.5 %-
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 207 160 4951
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg0.86

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