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- PDB-1p32: CRYSTAL STRUCTURE OF HUMAN P32, A DOUGHNUT-SHAPED ACIDIC MITOCHON... -

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Basic information

Entry
Database: PDB / ID: 1p32
TitleCRYSTAL STRUCTURE OF HUMAN P32, A DOUGHNUT-SHAPED ACIDIC MITOCHONDRIAL MATRIX PROTEIN
ComponentsMITOCHONDRIAL MATRIX PROTEIN, SF2P32
KeywordsMITOCHONDRIAL MATRIX PROTEIN
Function / homology
Function and homology information


adrenergic receptor binding / Apoptotic factor-mediated response / Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function / kininogen binding / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / mitochondrial ribosome binding / deoxyribonuclease inhibitor activity / C5-methylcytidine-containing RNA reader activity / positive regulation of dendritic cell chemotaxis ...adrenergic receptor binding / Apoptotic factor-mediated response / Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function / kininogen binding / negative regulation of MDA-5 signaling pathway / negative regulation of RIG-I signaling pathway / mitochondrial ribosome binding / deoxyribonuclease inhibitor activity / C5-methylcytidine-containing RNA reader activity / positive regulation of dendritic cell chemotaxis / negative regulation of defense response to virus / mitochondrial RNA catabolic process / hyaluronic acid binding / complement component C1q complex binding / positive regulation of trophoblast cell migration / positive regulation of mitochondrial translation / regulation of complement activation / negative regulation of interleukin-12 production / positive regulation of neutrophil chemotaxis / presynaptic active zone / transcription factor binding / RHOC GTPase cycle / negative regulation of mRNA splicing, via spliceosome / negative regulation of type II interferon production / RHOA GTPase cycle / complement activation, classical pathway / enzyme inhibitor activity / negative regulation of double-strand break repair via homologous recombination / Intrinsic Pathway of Fibrin Clot Formation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of cell adhesion / RNA splicing / protein kinase C binding / cytosolic ribosome assembly / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / mRNA processing / transcription corepressor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / positive regulation of apoptotic process / mitochondrial matrix / innate immune response / mRNA binding / apoptotic process / DNA damage response / nucleolus / glutamatergic synapse / cell surface / negative regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mitochondrial Matrix Protein; Chain A / Mitochondrial glycoprotein / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Roll / Alpha Beta
Similarity search - Domain/homology
Complement component 1 Q subcomponent-binding protein, mitochondrial / Complement component 1 Q subcomponent-binding protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJiang, J. / Zhang, Y. / Krainer, A.R. / Xu, R.-M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of human p32, a doughnut-shaped acidic mitochondrial matrix protein.
Authors: Jiang, J. / Zhang, Y. / Krainer, A.R. / Xu, R.M.
History
DepositionNov 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Aug 29, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.5Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MITOCHONDRIAL MATRIX PROTEIN, SF2P32
B: MITOCHONDRIAL MATRIX PROTEIN, SF2P32
C: MITOCHONDRIAL MATRIX PROTEIN, SF2P32


Theoretical massNumber of molelcules
Total (without water)71,4783
Polymers71,4783
Non-polymers00
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-44 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.625, 56.481, 93.831
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.309, 0.7076, -0.6355), (0.2477, 0.705, 0.6646), (0.9182, 0.0479, -0.3931)65.25, -25.357, -1.7757
2given(-0.3361, 0.6679, -0.664), (0.2521, 0.7431, 0.6199), (0.9075, 0.041, -0.4182)67.204, -23.9697, -0.4274
3given(-0.2941, 0.2941, 0.9094), (0.6977, 0.7164, -0.006), (-0.6532, 0.6327, -0.4159)27.801, -25.8699, 58.9629

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Components

#1: Protein MITOCHONDRIAL MATRIX PROTEIN, SF2P32


Mass: 23826.105 Da / Num. of mol.: 3 / Mutation: L74M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli / References: UniProt: MA32_HUMAN, UniProt: Q07021*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.16 Å3/Da / Density % sol: 44.5 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
210 %glycerol1reservoir
325 %MPD1reservoir
45-10 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95,0.9786,0.9789,1.0
DetectorType: BRANDEIS / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.97861
30.97891
411
ReflectionResolution: 2.25→50 Å / Num. obs: 27284 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.045 / Rsym value: 0.107 / Net I/σ(I): 15.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.139 / % possible all: 59.8
Reflection
*PLUS
Num. measured all: 170171
Reflection shell
*PLUS
% possible obs: 59.8 %

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Details: INITIALLY THE MODEL WAS REFINED BY XPLOR
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1327 4.5 %RANDOM
Rwork0.173 ---
obs-26812 91.7 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 56.0793 Å2 / ksol: 0.359245 e/Å3
Displacement parametersBiso mean: 35.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.787 Å20 Å2-0.58 Å2
2---4.65 Å20 Å2
3---2.871 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 0 398 4663
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.18
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.5631.5
X-RAY DIFFRACTIONx_mcangle_it8.32
X-RAY DIFFRACTIONx_scbond_it7.8472
X-RAY DIFFRACTIONx_scangle_it11.1792.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.25→2.33 Å
RfactorNum. reflection% reflection
Rfree0.2667 72 2.46 %
Rwork0.1926 1655 -
obs--59.04 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor obs: 0.1926

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