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- PDB-3mvc: High resolution crystal structure of the heme domain of GLB-6 fro... -

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Basic information

Entry
Database: PDB / ID: 3mvc
TitleHigh resolution crystal structure of the heme domain of GLB-6 from C. elegans
ComponentsGlobin protein 6
KeywordsELECTRON TRANSPORT / GLOBIN / OXYGEN SENSOR / HEME-BINDING PROTEIN / C. ELEGANS / OXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen transport / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding
Similarity search - Function
: / Myoglobin-like, M family globin domain / 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 / NITRATE ION / PRASEODYMIUM ION / Globin-like protein 6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.401 Å
AuthorsYoon, J. / Herzik Jr, M.A. / Winter, M.B. / Tran, R. / Olea Jr, C. / Marletta, M.A.
CitationJournal: Biochemistry / Year: 2010
Title: Structure and properties of a bis-histidyl ligated globin from Caenorhabditis elegans.
Authors: Yoon, J. / Herzik, M.A. / Winter, M.B. / Tran, R. / Olea, C. / Marletta, M.A.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_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_seq_id / _struct_conn.ptnr1_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: Globin protein 6
B: Globin protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,04217
Polymers37,6872
Non-polymers2,35515
Water2,486138
1
A: Globin protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,25511
Polymers18,8441
Non-polymers1,41110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Globin protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7876
Polymers18,8441
Non-polymers9435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.582, 76.347, 62.696
Angle α, β, γ (deg.)90.00, 91.76, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

#1: Protein Globin protein 6


Mass: 18843.527 Da / Num. of mol.: 2 / Fragment: Globin 6 heme domain 195-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: N2 / Gene: C18C4.9, glb-6 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q18086
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pr
#4: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.0 M NaNO3 and 0.1 M Na(CH3COO) pH 4.5) and 1 ul of 10 mM praseodymium (III) acetate solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.1158
SYNCHROTRONALS 5.0.320.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2009
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11581
20.97651
ReflectionResolution: 1.4→50 Å / Num. all: 12 / Num. obs: 130779 / % possible obs: 98.34 % / Redundancy: 4.2 % / Rsym value: 0.048 / Net I/σ(I): 21.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4 % / Num. unique all: 3273 / Rsym value: 0.294 / % possible all: 95.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.401→33.705 Å / SU ML: 0.18 / σ(F): 0.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 6482 5.1 %
Rwork0.1607 --
obs0.1629 127214 92.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.661 Å2 / ksol: 0.429 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.7077 Å20 Å2-1.1109 Å2
2---2.1296 Å20 Å2
3----3.5781 Å2
Refinement stepCycle: LAST / Resolution: 1.401→33.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 126 138 2789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052726
X-RAY DIFFRACTIONf_angle_d0.8543698
X-RAY DIFFRACTIONf_dihedral_angle_d16.157975
X-RAY DIFFRACTIONf_chiral_restr0.057375
X-RAY DIFFRACTIONf_plane_restr0.004476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4012-1.41720.26472170.18813409X-RAY DIFFRACTION80
1.4172-1.43380.22951780.18043609X-RAY DIFFRACTION84
1.4338-1.45130.25522450.1613711X-RAY DIFFRACTION85
1.4513-1.46970.20271740.14433770X-RAY DIFFRACTION87
1.4697-1.4890.25631660.14543824X-RAY DIFFRACTION88
1.489-1.50940.18361940.14193884X-RAY DIFFRACTION89
1.5094-1.5310.21731880.14693851X-RAY DIFFRACTION89
1.531-1.55380.22432030.13913900X-RAY DIFFRACTION90
1.5538-1.57810.19472260.14083944X-RAY DIFFRACTION91
1.5781-1.6040.2242140.13853936X-RAY DIFFRACTION91
1.604-1.63170.17592170.13144022X-RAY DIFFRACTION93
1.6317-1.66130.20172450.14283995X-RAY DIFFRACTION93
1.6613-1.69330.22232200.13334086X-RAY DIFFRACTION94
1.6933-1.72780.1861910.13544070X-RAY DIFFRACTION94
1.7278-1.76540.20772530.13384057X-RAY DIFFRACTION94
1.7654-1.80650.20612290.12564132X-RAY DIFFRACTION95
1.8065-1.85160.16452360.12744158X-RAY DIFFRACTION96
1.8516-1.90170.2162370.13694152X-RAY DIFFRACTION96
1.9017-1.95770.19642620.13324117X-RAY DIFFRACTION96
1.9577-2.02080.19381910.13124230X-RAY DIFFRACTION97
2.0208-2.09310.15961900.13314279X-RAY DIFFRACTION97
2.0931-2.17680.17562400.13524130X-RAY DIFFRACTION97
2.1768-2.27590.21482040.13934188X-RAY DIFFRACTION97
2.2759-2.39590.1642200.15084243X-RAY DIFFRACTION97
2.3959-2.54590.23422660.16064161X-RAY DIFFRACTION97
2.5459-2.74240.18651970.17074248X-RAY DIFFRACTION97
2.7424-3.01820.19492190.17114226X-RAY DIFFRACTION98
3.0182-3.45460.22742140.17724234X-RAY DIFFRACTION97
3.4546-4.3510.20182470.16184130X-RAY DIFFRACTION96
4.351-33.71510.20451990.19744036X-RAY DIFFRACTION93

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