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- PDB-3quw: Crystal structure of yeast Mmf1 -

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Basic information

Entry
Database: PDB / ID: 3quw
TitleCrystal structure of yeast Mmf1
ComponentsProtein MMF1
KeywordsPROTEIN BINDING / chorismate mutase fold / intact mitochondria maintenance / Mitochondrial protein
Function / homology
Function and homology information


organonitrogen compound catabolic process / deaminase activity / isoleucine biosynthetic process / mitochondrial translation / mitochondrial matrix / mitochondrion / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein MMF1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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Assembly

Deposited unit
A: Protein MMF1


Theoretical massNumber of molelcules
Total (without water)16,9431
Polymers16,9431
Non-polymers00
Water1,38777
1
A: Protein MMF1

A: Protein MMF1

A: Protein MMF1


Theoretical massNumber of molelcules
Total (without water)50,8303
Polymers50,8303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5560 Å2
ΔGint-34 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.618, 77.618, 43.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-167-

HOH

21A-176-

HOH

31A-202-

HOH

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Components

#1: Protein Protein MMF1 / Isoleucine biosynthesis and maintenance of intact mitochondria 1 / Maintenance of mitochondrial function 1


Mass: 16943.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IBM1, MMF1, YIL051C / Plasmid: p28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P40185
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 25% polyethylene glycol 3550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97012 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97012 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 9969 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 14.8
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 7.2 / Num. unique all: 929 / Rsym value: 0.25 / % possible all: 94.5

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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 1JD1

1jd1


Resolution: 1.75→38.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.768 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 483 4.8 %RANDOM
Rwork0.18114 ---
obs0.18303 9481 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.841 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å2-0.79 Å20 Å2
2---1.59 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 0 77 1034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022977
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9531329
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8735124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16926.34141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03715163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.32151
X-RAY DIFFRACTIONr_chiral_restr0.0850.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021733
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_it0.7561.5629
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57421023
X-RAY DIFFRACTIONr_scbond_it2.6033348
X-RAY DIFFRACTIONr_scangle_it4.2844.5306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 32 -
Rwork0.245 650 -
obs--93.3 %

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