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- PDB-2w31: globin domain of Geobacter sulfurreducens globin-coupled sensor -

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Basic information

Entry
Database: PDB / ID: 2w31
Titleglobin domain of Geobacter sulfurreducens globin-coupled sensor
ComponentsGLOBIN
KeywordsOXYGEN TRANSPORT / GEOBACTER SULFURREDUCENS / HEXACOORDINATION / GLOBIN COUPLED SENSOR
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Phosphate-starvation-induced PsiE-like / Phosphate-starvation-inducible E family / Globin-sensor domain / Protoglobin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Heme-binding sensor globin domain protein
Similarity search - Component
Biological speciesGEOBACTER SULFURREDUCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsPesce, A. / Thijs, L. / Nardini, M. / Desmet, F. / Sisinni, L. / Gourlay, L. / Bolli, A. / Coletta, M. / Van Doorslaer, S. / Wan, X. ...Pesce, A. / Thijs, L. / Nardini, M. / Desmet, F. / Sisinni, L. / Gourlay, L. / Bolli, A. / Coletta, M. / Van Doorslaer, S. / Wan, X. / Alam, M. / Ascenzi, P. / Moens, L. / Bolognesi, M. / Dewilde, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Hise11 and Hisf8 Provide Bis-Histidyl Heme Hexa-Coordination in the Globin Domain of Geobacter Sulfurreducens Globin-Coupled Sensor.
Authors: Pesce, A. / Thijs, L. / Nardini, M. / Desmet, F. / Sisinni, L. / Gourlay, L. / Bolli, A. / Coletta, M. / Van Doorslaer, S. / Wan, X. / Alam, M. / Ascenzi, P. / Moens, L. / Bolognesi, M. / Dewilde, S.
History
DepositionNov 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLOBIN
B: GLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8917
Polymers38,3812
Non-polymers1,5095
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-2.2 kcal/mol
Surface area17270 Å2
MethodPQS
Unit cell
Length a, b, c (Å)56.634, 73.830, 89.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLOBIN


Mass: 19190.734 Da / Num. of mol.: 2
Fragment: GLOBIN DOMAIN OF GLOBIN COUPLED SENSOR, RESIDUES 1-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACTER SULFURREDUCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q747F6
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growTemperature: 277 K / pH: 6.5
Details: 10% PEG 4000, 0.1 M MES PH 6.5, 0.2 M MGCL2, AT 277 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.837
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.837 Å / Relative weight: 1
ReflectionResolution: 1.5→38.4 Å / Num. obs: 60673 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.5→34.14 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.43 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM 153 TO 162 WERE DISORDERED AND WERE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.207 6136 10.1 %RANDOM
Rwork0.164 ---
obs0.168 54467 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 104 399 3025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222829
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4432.0513868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3695334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20723.613155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77215499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5211526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022206
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21435
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21938
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8931.51625
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39322552
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.31131373
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6624.51296
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 419
Rwork0.159 4028

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