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- PDB-3qv0: Crystal structure of Saccharomyces cerevisiae Mam33 -

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Basic information

Entry
Database: PDB / ID: 3qv0
TitleCrystal structure of Saccharomyces cerevisiae Mam33
ComponentsMitochondrial acidic protein MAM33
KeywordsPROTEIN BINDING / a bowl like structure / mitochondrial oxidative phosphorylation
Function / homology
Function and homology information


translation activator activity / mitochondrial ribosome binding / positive regulation of mitochondrial translation / aerobic respiration / mitochondrial matrix / mRNA binding / mitochondrion
Similarity search - Function
Mitochondrial Matrix Protein; Chain A / Mitochondrial glycoprotein / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Roll / Alpha Beta
Similarity search - Domain/homology
Mitochondrial acidic protein MAM33
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJiang, Y.L. / Pu, Y.G. / Ma, X.X. / Chen, Y. / Zhou, C.Z.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structures and putative interface of Saccharomyces cerevisiae mitochondrial matrix proteins Mmf1 and Mam33.
Authors: Pu, Y.G. / Jiang, Y.L. / Ye, X.D. / Ma, X.X. / Guo, P.C. / Lian, F.M. / Teng, Y.B. / Chen, Y. / Zhou, C.Z.
History
DepositionFeb 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 acidic protein MAM33


Theoretical massNumber of molelcules
Total (without water)25,8751
Polymers25,8751
Non-polymers00
Water1,56787
1
A: Mitochondrial acidic protein MAM33

A: Mitochondrial acidic protein MAM33

A: Mitochondrial acidic protein MAM33


Theoretical massNumber of molelcules
Total (without water)77,6253
Polymers77,6253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6950 Å2
ΔGint-53 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.755, 118.755, 118.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Mitochondrial acidic protein MAM33


Mass: 25875.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAM33, YIL070C / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40513
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 20% Polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9194 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.1→83.97 Å / Num. obs: 16404 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 37.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 21.3 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 10.3 / Num. unique all: 1605 / Rsym value: 0.393 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1P32

1p32


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.361 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25219 830 5.1 %RANDOM
Rwork0.22741 ---
obs0.22866 15573 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.453 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 0 87 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221469
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9571983
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0775175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74825.69679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90715254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.174155
X-RAY DIFFRACTIONr_chiral_restr0.0710.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211128
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_it0.6191.5892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1921437
X-RAY DIFFRACTIONr_scbond_it1.7753577
X-RAY DIFFRACTIONr_scangle_it2.9664.5546
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 63 -
Rwork0.207 1149 -
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)
12.3659-0.0218-0.87590.794-0.48571.540.02180.1013-0.0442-0.26390.01770.10030.0637-0.2388-0.03950.20540.0226-0.0490.1232-0.00630.1063-5.51818.383-5.377
20.53970.3329-0.63140.6484-0.84311.9394-0.00760.113-0.1006-0.1850.03170.0650.0527-0.1939-0.02410.20240.0571-0.01890.1709-0.01610.1633-5.23118.172-4.229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 266
2X-RAY DIFFRACTION2A301 - 387

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