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- PDB-4b0y: Determination of X-ray Structure of human SOUL by Molecular Repla... -

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Basic information

Entry
Database: PDB / ID: 4b0y
TitleDetermination of X-ray Structure of human SOUL by Molecular Replacement
ComponentsHEME-BINDING PROTEIN 2
KeywordsAPOPTOSIS
Function / homology
Function and homology information


azurophil granule lumen / heme binding / Neutrophil degranulation / mitochondrion / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
SOUL haem-binding protein / SOUL heme-binding protein / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Heme-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsFreire, F. / Carvalho, A.L. / Aveiro, S.S. / Charbonnier, P. / Moulis, J.M. / Romao, M.J. / Goodfellow, B.J. / Macedo, A.L.
CitationJournal: To be Published
Title: Human Soul: A Heme-Binding or a Bh3 Domain-Containing Protein
Authors: Freire, F. / Carvalho, A.L. / Aveiro, S.S. / Charbonnier, P. / Moulis, J.M. / Romao, M.J. / Goodfellow, B.J. / Macedo, A.L.
History
DepositionJul 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEME-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)25,5501
Polymers25,5501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.670, 144.670, 60.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein HEME-BINDING PROTEIN 2 / PLACENTAL PROTEIN 23 / PP23 / PROTEIN SOUL


Mass: 25550.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y5Z4

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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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 6.5 / Details: 2 M AMMONIUM SULPHATE, 0.1 M MES 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 3.5→47.35 Å / Num. obs: 5025 / % possible obs: 100 % / Observed criterion σ(I): 6.2 / Redundancy: 30.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 24.6
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 32.2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AYZ

4ayz


Resolution: 3.5→47.35 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.809 / SU B: 61.251 / SU ML: 0.435 / Cross valid method: THROUGHOUT / ESU R: 1.273 / ESU R Free: 0.586
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30638 484 9.6 %RANDOM
Rwork0.27046 ---
obs0.2739 4541 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.441 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å2-0.72 Å20 Å2
2---1.44 Å20 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 3.5→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 0 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221295
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8461.9421770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7265166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9224.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.615178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.864154
X-RAY DIFFRACTIONr_chiral_restr0.0510.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211002
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 36 -
Rwork0.304 323 -
obs--100 %
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)
17.88720.2766-3.3726-0.319-3.639912.4884-0.43080.7688-0.96210.2784-0.2876-0.3596-0.59790.39780.71840.46220.0176-0.09050.2273-0.11390.322815.9372-62.2818-2.5441
237.04194.1057-9.96120.9555-2.919811.7728-0.35871.41310.7274-0.29290.0090.1752-0.01920.04370.34970.25080.0678-0.20040.07790.00420.172318.9902-56.0322-0.2511
36.04412.68271.66724.7899-0.34313.13640.5449-0.69940.37280.5444-0.42180.4420.5736-0.3904-0.12310.2138-0.01240.03030.2402-0.01080.066913.5052-62.710419.5824
410.894521.2071-10.934313.0336-4.1199-4.22160.18030.39770.9155-0.03290.18330.55250.1476-0.0341-0.36360.23630.0672-0.07770.546-0.06170.3898-0.8741-71.293714.7986
51.2574-1.70170.4832-2.6622-4.81566.4329-0.30440.1274-0.0694-0.0544-0.13230.06110.46740.48630.43670.11130.0701-0.06480.1595-0.04010.347514.9719-59.932912.8032
69.1082-0.22775.4939-0.1903-1.04847.32350.44690.3132-0.26370.04780.2084-0.091-0.0856-0.3466-0.65530.12840.0338-0.060.1889-0.01580.280311.8298-59.614613.2712
7-2.3521-1.6695-4.954223.1077-4.7807-13.2008-0.0612-0.037-0.1307-0.1622-0.06990.82960.38840.1050.13110.0583-0.0528-0.01590.52740.0840.5015-1.3008-63.039713.0875
87.18481.238-2.39981.1952-0.88415.84990.2467-0.275-0.0735-0.3978-0.11240.4331-0.16680.1684-0.13440.19930.0244-0.17630.044-0.03150.167717.434-57.69968.2032
95.86038.1973-5.429520.2308-15.812512.08350.1282-0.0115-0.19220.6111-0.2184-0.4544-0.59930.49750.09020.22580.04760.00750.4718-0.09470.255531.8244-52.3948.9289
106.8060.16062.02620.4414-1.47216.3838-0.2053-0.1093-0.0084-0.1626-0.0388-0.46150.08230.1660.24410.04650.02380.08280.11250.02420.277322.4383-57.14077.8187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 29
2X-RAY DIFFRACTION2A36 - 47
3X-RAY DIFFRACTION3A48 - 73
4X-RAY DIFFRACTION4A74 - 82
5X-RAY DIFFRACTION5A83 - 97
6X-RAY DIFFRACTION6A100 - 116
7X-RAY DIFFRACTION7A117 - 125
8X-RAY DIFFRACTION8A126 - 146
9X-RAY DIFFRACTION9A147 - 167
10X-RAY DIFFRACTION10A168 - 197

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