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- PDB-4mpm: Wild-type human neuroglobin -

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Basic information

Entry
Database: PDB / ID: 4mpm
TitleWild-type human neuroglobin
ComponentsNeuroglobin
KeywordsAPOPTOSIS / globin / oxygen supply / nitrite reductase / proto-porphyrin IX / brain neurons
Function / homology
Function and homology information


Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / oxygen binding / cellular response to hypoxia / response to hypoxia / mitochondrial matrix ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / 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 domain profile. / Globin-like / Globin / Globin / 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 / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsGuimaraes, B.G. / Golinelli-Pimpaneau, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The crystal structure of wild-type human brain neuroglobin reveals flexibility of the disulfide bond that regulates oxygen affinity.
Authors: Guimaraes, B.G. / Hamdane, D. / Lechauve, C. / Marden, M.C. / Golinelli-Pimpaneau, B.
History
DepositionSep 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Neuroglobin
B: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1364
Polymers33,9032
Non-polymers1,2332
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-55 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.150, 48.490, 39.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

21A-414-

HOH

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Components

#1: Protein Neuroglobin


Mass: 16951.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NGB / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9NPG2
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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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: 37.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium acetate, tetrahydrate, 0.1 M sodium cacodylate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.74→30 Å / Num. obs: 27784 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 6.22 % / Biso Wilson estimate: 18.65 Å2 / Rsym value: 0.131 / Net I/σ(I): 10.12
Reflection shellResolution: 1.74→1.85 Å / Redundancy: 5.79 % / Mean I/σ(I) obs: 2.41 / Rsym value: 0.71 / % possible all: 94.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJ6

1oj6


Resolution: 1.74→21.24 Å / Cor.coef. Fo:Fc: 0.9313 / Cor.coef. Fo:Fc free: 0.8979 / SU R Cruickshank DPI: 0.128 / Isotropic thermal model: OVERALL ANISOTROPIC B VALUE / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1389 5 %RANDOM
Rwork0.1814 ---
obs0.1837 27772 98.76 %-
Displacement parametersBiso mean: 20.29 Å2
Baniso -1Baniso -2Baniso -3
1--4.0655 Å20 Å20 Å2
2--0.0725 Å20 Å2
3---3.993 Å2
Refine analyzeLuzzati coordinate error obs: 0.198 Å
Refinement stepCycle: LAST / Resolution: 1.74→21.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 86 246 2655
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012490HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963412HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d820SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes381HARMONIC5
X-RAY DIFFRACTIONt_it2490HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.74→1.81 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2281 128 5.03 %
Rwork0.213 2419 -
all0.2138 2547 -
obs--98.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.28370.0242-0.19890.5180.20181.04020.0058-0.0307-0.0697-0.0413-0.0089-0.0010.03-0.09050.0031-0.1513-0.0067-0.0031-0.11910.0161-0.131712.8169-5.0869-7.9608
20.5506-0.2217-0.12650.6485-0.14190.630.02360.0616-0.0032-0.0319-0.0061-0.0174-0.0493-0.0296-0.0174-0.1091-0.017-0.0013-0.1077-0.0025-0.125427.095812.596-13.0555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|149 A|201 - A|201 }A3 - 149
2X-RAY DIFFRACTION1{ A|3 - A|149 A|201 - A|201 }A201
3X-RAY DIFFRACTION2{ B|2 - B|149 B|201 - B|201 }B2 - 149
4X-RAY DIFFRACTION2{ B|2 - B|149 B|201 - B|201 }B201

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