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- PDB-3vty: Crystal structure of MamA -

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Basic information

Entry
Database: PDB / ID: 3vty
TitleCrystal structure of MamA
ComponentsMamA
KeywordsPROTEIN BINDING / Tetratricopeptide repeats (TPR) containing protein / TPR proteins / protein-protein interactions / cytosol / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


Tetratricopeptide repeat / TPR repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Tetratricopeptide repeat / TPR repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCandidatus Magnetobacterium bavaricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsZeytuni, N. / Baran, D. / Davidov, G. / Zarivach, R.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Inter-phylum structural conservation of the magnetosome-associated TPR-containing protein, MamA
Authors: Zeytuni, N. / Baran, D. / Davidov, G. / Zarivach, R.
History
DepositionJun 8, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MamA
B: MamA
C: MamA
D: MamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,80810
Polymers82,5954
Non-polymers2136
Water10,881604
1
A: MamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6842
Polymers20,6491
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7203
Polymers20,6491
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6842
Polymers20,6491
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7203
Polymers20,6491
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-87 kcal/mol
Surface area31500 Å2
MethodPISA
6
A: MamA
D: MamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4045
Polymers41,2982
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-40 kcal/mol
Surface area17270 Å2
MethodPISA
7
B: MamA
C: MamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4045
Polymers41,2982
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-37 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.701, 101.315, 139.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer.

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Components

#1: Protein
MamA


Mass: 20648.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Magnetobacterium bavaricum (bacteria)
Strain: Mbav / Gene: MamA / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K7N5L8*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE OF THE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT ...THE SEQUENCE DATABASE OF THE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. RESIDUES 42 TO END OF THE ENTIRE PROTEIN WAS CLONED, N-TERMINAL RESIDUES MG (40-41) AND C-TERMINAL RESIDUES ELALVPR (217-223) WERE FROM EXPRESSION TAG.

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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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 0.1M Sodium Acetate pH 4.4, 1.75M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→81.99 Å / Num. all: 49963 / Num. obs: 49745 / % possible obs: 99.1 %
Reflection shellResolution: 2→2.03 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→81.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2005 / WRfactor Rwork: 0.1535 / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.8822 / SU B: 7.355 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1755 / SU Rfree: 0.1629 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 2523 5.1 %RANDOM
Rwork0.1625 ---
all0.1653 49963 --
obs0.1653 49745 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.47 Å2 / Biso mean: 21.2149 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2→81.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5528 0 6 604 6138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225724
X-RAY DIFFRACTIONr_bond_other_d0.0010.023991
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9897707
X-RAY DIFFRACTIONr_angle_other_deg1.1339819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97825.02245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.673151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6671521
X-RAY DIFFRACTIONr_chiral_restr0.1170.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026289
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021116
X-RAY DIFFRACTIONr_mcbond_it1.1511.53506
X-RAY DIFFRACTIONr_mcbond_other0.3061.51447
X-RAY DIFFRACTIONr_mcangle_it2.00425613
X-RAY DIFFRACTIONr_scbond_it3.2232218
X-RAY DIFFRACTIONr_scangle_it5.1654.52077
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 176 -
Rwork0.186 3367 -
all-3543 -
obs--96.54 %
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)
10.40310.22370.13560.15360.13660.19390.0083-0.0387-0.0378-0.0065-0.0218-0.0245-0.0009-0.01160.01350.03910.00740.00690.03220.01410.065612.977744.842416.8454
20.2743-0.18370.03480.1658-0.12660.3089-0.06410.0464-0.05590.0216-0.03710.01420.0450.00370.10120.0416-0.00940.03510.0262-0.02320.0784-1.677243.6332-14.1287
30.1534-0.2284-0.12660.35420.12950.3585-0.01730.038-0.01410.0291-0.06010.0043-0.0046-0.02710.07740.0366-0.00840.00150.0486-0.01480.042813.253356.9737-15.837
40.1760.2273-0.05240.3076-0.12010.5270.0026-0.0445-0.0163-0.0068-0.0629-0.0099-0.03210.01580.06030.02450.0219-0.01110.04890.0050.0508-1.528358.850417.458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 216
2X-RAY DIFFRACTION2B42 - 216
3X-RAY DIFFRACTION3C42 - 219
4X-RAY DIFFRACTION4D46 - 216

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